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Journal of Chemical Information and Modeling, Volume 63
Volume 63, Number 1, January 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
:
Editorial: Machine Learning in Bio-cheminformatics. 1 - Martin Stroet
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. 2-8 - Ahmet Yildirim, Mustafa Tekpinar
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins. 9-19 - Rui P. P. Neves
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. 20-26 - Daniel Vella
Few-Shot Learning for Low-Data Drug Discovery. 27-42 - Weimin Zhu, Yi Zhang, Duancheng Zhao, Jianrong Xu, Ling Wang
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention. 43-55 - Maria Vittoria Togo
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity. 56-66 - Hao Tian
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. 67-75 - Ryo Kawada
Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. 76-86 - Omer Kaspi, Osnat Israelsohn-Azulay, Zidon Yigal, Hila Rosengarten, Matea Krmpotic
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments. 87-100 - Jörg Heider
Apo2ph4: A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening. 101-110 - Teng-Zhi Long
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. 111-125 - Omri Wolk
Predicting the Likelihood of Molecules to Act as Modulators of Protein-Protein Interactions. 126-137 - Daniel Sethio
Simulation Reveals the Chameleonic Behavior of Macrocycles. 138-146 - Paul L. Türtscher, Markus Reiher
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach. 147-160 - Mirko Paulikat
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. 161-172 - Chen Qian, Xin Zhou, Jessica Rehmel
Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk. 173-186 - Andrey I. Frolov
pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. 187-196 - Oriol Gracia Carmona
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. 197-207 - Chythra J. N.
Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. 208-223 - Nibedita Ray Chaudhuri, Shubhra Ghosh Dastidar
Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. 224-239 - Kei Moritsugu
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. 240-250 - Francesco Pettini
Early Steps in C-Type Inactivation of the hERG Potassium Channel. 251-258 - Ryuhei Harada
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. 259-269 - Leslie Sánchez
Elucidation of the Reaction Mechanism of Cavia porcellus l-Asparaginase: A QM/MM Study. 270-280 - Till El Harrar
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. 281-298 - Anastasiia Delova, Raúl Losantos
Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin. 299-307 - Yuying Liu, Ying Wang, Yu Zhang, Yu Zou, Guanghong Wei
Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. 308-320 - Aristarc Suriñach, Adam Hospital
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. 321-334 - Jiahui Chen
Emerging Dominant SARS-CoV-2 Variants. 335-342 - Luca Torielli
Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. 343-353 - Madelyn Smith
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. 354-361 - Xiaoyue Ji, Hao Liu
Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. 362-374 - Reem A. Alkhodier
Comparison of Conformational Analyses of Naturally Occurring Flavonoid-O-Glycosides with Unnatural Flavonoid-CF2-Glycosides Using Molecular Modeling. 375-386 - Marley L. Samways
Water Networks in Complexes between Proteins and FDA-Approved Drugs. 387-396 - Yan Liu, He Yan, Long-Chen Shen
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. 397-405 - Stefano Costanzi
Correction to "Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis". 406
Volume 63, Number 2, January 2023
- Diego Enry Barreto Gomes
ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies. 407-411 - Kristian Kríz
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. 412-431 - Raghad Al-Jarf, Simon Tang
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. 432-441 - Raya Stoyanova, Paul Maximilian Katzberger, Leonid Komissarov
Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage. 442-458 - Cesare Roncaglia
Machine Learning Assisted Clustering of Nanoparticle Structures. 459-473 - Iori Azuma, Tadahaya Mizuno
NRBdMF: A Recommendation Algorithm for Predicting Drug Effects Considering Directionality. 474-483 - Ye Buehler
Molecular Framework Analysis of the Generated Database GDB-13s. 484-492 - Yangcheng Ai, Zichao Yang, Zilong Yang
Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine. 493-506 - Sebastián Adolfo Cuesta, Martín Moreno
ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms. 507-521 - Reecan J. Juarez, Yaoyukun Jiang
LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. 522-530 - Luca Mollica
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. 531-545 - Alexander Zlobin
Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. 546-560 - Yishui Li, Runduo Liu, Jie Liu, Haibin Luo, Chengkun Wu, Zhe Li
An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. 561-570 - Namita Dube, Sabab Hasan Khan
Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. 571-582 - Filipp Gusev
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. 583-594 - Federico N. Pedron
Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. 595-604 - Xiaokun Hong
Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. 605-618 - Jie Gao
Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation. 619-632 - Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2. 633-642 - Ke Zuo, Riccardo Capelli
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. 643-654 - Zakir Ali
Structural and Energetic Features of Base-Base Stacking Contacts in RNA. 655-669 - Rojalin Pradhan, Sibarama Panigrahi
Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. 670-690
Volume 63, Number 3, February 2023
- Fabio Urbina, Filippa Lentzos, Cédric Invernizzi
Preventing AI From Creating Biochemical Threats. 691-694 - Yan A. Ivanenkov
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization. 695-701 - Cécile Hilpert
Facilitating CG Simulations with MAD: The MArtini Database Server. 702-710 - Madushanka Manathunga
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. 711-717 - Mateusz K. Bieniek
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. 718-724 - Adem R. N. Aouichaoui
Combining Group-Contribution Concept and Graph Neural Networks Toward Interpretable Molecular Property Models. 725-744 - Lincan Fang, Xiaomi Guo, Milica Todorovic
Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization. 745-752 - Frank W. Marrs
Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives. 753-769 - Yixiang Ruan
AROPS: A Framework of Automated Reaction Optimization with Parallelized Scheduling. 770-781 - Donghan Wang
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion. 782-793 - Kohei Nemoto, Hiromasa Kaneko
De Novo Direct Inverse QSPR/QSAR: Chemical Variational Autoencoder and Gaussian Mixture Regression Models. 794-805 - Yufeng Liu
Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models. 806-814 - Yuqing Yang, Dongping Liu, Zhendong Hua, Peng Xu, Youmei Wang, Bin Di
Machine Learning-Assisted Rapid Screening of Four Types of New Psychoactive Substances in Drug Seizures. 815-825 - Adnan Khan, Jamal Uddin, Farman Ali
AFP-SPTS: An Accurate Prediction of Antifreeze Proteins Using Sequential and Pseudo-Tri-Slicing Evolutionary Features with an Extremely Randomized Tree. 826-834 - Haiping Zhang
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. 835-845 - Tuan Xu, Md Kabir, Srilatha Sakamuru
Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. 846-855 - Seungchan An
Computational Prediction of the Phenotypic Effect of Flavonoids on Adiponectin Biosynthesis. 856-869 - Sneha Thomas, Kevin S. Silmore
Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices. 870-881 - Álvaro Pérez-Barcia, Gustavo Cárdenas, Juan J. Nogueira
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. 882-897 - Francesca Peccati
Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. 898-909 - Abhishek Acharya
Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. 910-927 - Efpraxia Tzortzini
Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. 928-949 - Santiago Movilla
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. 950-958 - Krishna Prasad Ghanta
Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. 959-972 - Patrice Koehl
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives. 973-985 - Yazdan Maghsoud
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. 986-1001 - Saikat Pal
Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. 1002-1011 - Adam Stasiulewicz
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. 1012-1027 - Horrick Sharma, Pragya Sharma, Uzziah Urquiza, Lerin R. Chastain, Michael A. Ihnat:
Exploration of a Large Virtual Chemical Space: Identification of Potent Inhibitors of Lactate Dehydrogenase-A against Pancreatic Cancer. 1028-1043 - Jun Hu
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. 1044-1057 - Kai Kang
ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. 1058-1065 - Ran Liu, Xiang Liu
Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction. 1066-1075 - Xue-Qiang Fan, Bing Lin, Jun Hu, Zhong-Yi Guo
I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning. 1076-1086
Volume 63, Number 4, February 2023
- Darya Stepanenko, Stephanie Budhan, Carlos Simmerling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. 1087-1092 - Jan-Oliver Felix Kapp-Joswig
CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. 1093-1098 - Jonathan G. M. Conn, James W. Carter, Justin J. A. Conn, Vigneshwari Subramanian
Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models. 1099-1113 - Mohammadamin Tavakoli, Yin Ting T. Chiu
RMechDB: A Public Database of Elementary Radical Reaction Steps. 1114-1123 - Sergei A. Evteev
SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein-Ligand-Binding Sites. 1124-1132 - Jintu Zhang
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. 1133-1142 - Jiali Guo, Ming Sun, Xueyan Zhao, Chaojie Shi, Haoming Su, Yanzhi Guo, Xuemei Pu
General Graph Neural Network-Based Model To Accurately Predict Cocrystal Density and Insight from Data Quality and Feature Representation. 1143-1156 - José Manuel Vásquez-Pérez
A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters. 1157-1165 - Benjamin I. Tingle, Khanh G. Tang, Mar Castanon, John J. Gutierrez, Munkhzul Khurelbaatar, Chinzorig Dandarchuluun, Yurii S. Moroz, John J. Irwin
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. 1166-1176 - Mengxian Yu, Yajuan Shi, Qingzhu Jia, Qiang Wang, Zheng-Hong Luo
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction. 1177-1187 - Bumjoon Seo
Evidence That Less Can Be More for Transferable Force Fields. 1188-1195 - Zoe Li
Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures. 1196-1207 - Sara Gómez
UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. 1208-1217 - Brad Crawford
MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. 1218-1228 - Lokesh Baweja, Jeff Wereszczynski
Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks. 1229-1238 - Timofey V. Losev
Quantum Mechanical-Cluster Approach to Solve the Bioisosteric Replacement Problem in Drug Design. 1239-1248 - Veronika Temml
Combination of In Silico and In Vitro Screening to Identify Novel Glutamate Carboxypeptidase II Inhibitors. 1249-1259 - Raffaele Fiorentini
Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins. 1260-1275 - Mohammad Khavani
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. 1276-1292 - Florian Karl Schackert
Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. 1293-1300 - Kemel Arafet
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents. 1301-1312 - Lihua Dong
Catalytic Mechanism of Pyridoxal 5′-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study. 1313-1322 - Pengyu Wang, Jun Zhang, Shengyu Zhang
Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes. 1323-1337 - Jeisson D. Corredor, Camilo Febres-Molina, Gonzalo A. Jaña
Insight into the Role of Active Site Protonation States and Water Molecules in the Catalytic Inhibition of DPP4 by Vildagliptin. 1338-1350 - Viet Hoang Man
Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2. 1351-1361 - Zheng Zhao
Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. 1362-1370 - Naila Zaman
Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets. 1371-1385 - Sergio Alejandro Poveda-Cuevas
NS1 from Two Zika Virus Strains Differently Interact with a Membrane: Insights to Understand Their Differential Virulence. 1386-1400
Volume 63, Number 5, March 2023
- Viet-Khoa Tran-Nguyen
Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons. 1401-1405 - Bharath Raghavan
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. 1406-1412 - Steve Agajanian, Mohammed Alshahrani, Fang Bai
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. 1413-1428 - Yeajee Kwon, Sera Park
BEAR: A Novel Virtual Screening Method Based on Large-Scale Bioactivity Data. 1429-1437 - Rajendra P. Joshi, Katherine J. Schultz
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. 1438-1453 - Esteban Marques
Improving Accuracy and Transferability of Machine Learning Chemical Activation Energies by Adding Electronic Structure Information. 1454-1461 - Andrew D. McNaughton
Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. 1462-1471 - Zailiang Zhu, Bozheng Dou, Yukang Cao, Jian Jiang, Yueying Zhu, Dong Chen, Hongsong Feng
TIDAL: Topology-Inferred Drug Addiction Learning. 1472-1489 - Renne Leini
In Silico Evaluation of the Thr58-Associated Conserved Water with KRAS Switch-II Pocket Binders. 1490-1505 - Luan Carvalho Martins
Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism. 1506-1520 - Inacrist Geronimo
On the Role of Molecular Conformation of the 8-Oxoguanine Lesion in Damaged DNA Processing by Polymerases. 1521-1528 - Yutaka Maruyama
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation. 1529-1541 - Souvik Mondal
Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid β Components of α-Synuclein. 1542-1555 - Beata Dulko-Smith, Pedro Ojeda-May, Jörgen Ådén
Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. 1556-1569 - Sweta Pradhan, Rajendra Rath, Mithun Biswas
GB1 Dimerization in Crowders: A Multiple Resolution Approach. 1570-1577 - Asma Gholami, Dariush Minai-Tehrani
Structural Insights into Pseudomonas aeruginosa Exotoxin A-Elongation Factor 2 Interactions: A Molecular Dynamics Study. 1578-1591 - Ya Gao
Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. 1592-1601 - Ge Song
Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. 1602-1614 - Hong-Quan Xu, Wei Zhang
Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics. 1615-1625 - Wei Hu
MecDDI: Clarified Drug-Drug Interaction Mechanism Facilitating Rational Drug Use and Potential Drug-Drug Interaction Prediction. 1626-1636 - Dmitrij Rappoport
Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves. 1637-1648
Volume 63, Number 6, March 2023
- Cayque Monteiro Castro Nascimento
Do Large Language Models Understand Chemistry? A Conversation with ChatGPT. 1649-1655 - Yuqi Zhang
Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery. 1656-1667 - Anna M. Díaz-Rovira
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. 1668-1674 - Noah R. Flynn
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity. 1675-1694 - Matthew R. Masters, Amr H. Mahmoud, Yao Wei, Markus A. Lill
Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility. 1695-1707 - Kamal Choudhary
AtomVision: A Machine Vision Library for Atomistic Images. 1708-1722 - Hamid Teimouri, Angela Medvedeva, Anatoly B. Kolomeisky
Bacteria-Specific Feature Selection for Enhanced Antimicrobial Peptide Activity Predictions Using Machine-Learning Methods. 1723-1733 - Emma P. Tysinger
Can We Quickly Learn to "Translate" Bioactive Molecules with Transformer Models? 1734-1744 - Brandon J. Bongers
Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. 1745-1755 - Zheyu Hu, Yaolin Guo, Zhen Liu, Diwei Shi, Yifan Li, Yu Hu, Moran Bu, Kan Luo, Jian He, Chong Wang, Shiyu Du:
AisNet: A Universal Interatomic Potential Neural Network with Encoded Local Environment Features. 1756-1765 - Marianne Rooman, Fabrizio Pucci
Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules. 1766-1775 - Mary Pitman
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. 1776-1793 - Emília P. Barros
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. 1794-1805 - Katarzyna Walczewska-Szewc
Structural Insights into ATP-Sensitive Potassium Channel Mechanics: A Role of Intrinsically Disordered Regions. 1806-1818 - Saheb Dutta, Amalendu Chandra
A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase. 1819-1832
Volume 63, Number 7, April 2023
- Xiaolin Pan
MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution. 1833-1840 - Samuel Genheden
AiZynthTrain: Robust, Reproducible, and Extensible Pipelines for Training Synthesis Prediction Models. 1841-1846 - Nikita Ionov
Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants. 1847-1851 - Andrew J. Hoover
Matcher: An Open-Source Application for Translating Large Structure/Property Data Sets into Insights for Drug Design. 1852-1857 - Althea T. Hansel-Harris
Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. 1858-1864 - Vishu Gupta, Kamal Choudhary
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction. 1865-1871 - Max Müller, Alexander Hagg
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization. 1872-1881 - Dibyajyoti Das, Broto Chakrabarty, Rajgopal Srinivasan, Arijit Roy
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures. 1882-1893 - Zaiyun Lin, Shiqiu Yin
G2GT: Retrosynthesis Prediction with Graph-to-Graph Attention Neural Network and Self-Training. 1894-1905 - Zaw-Myo Win
Using Machine Learning To Predict Partition Coefficient (Log P) and Distribution Coefficient (Log D) with Molecular Descriptors and Liquid Chromatography Retention Time. 1906-1913 - Fernando Jaume-Santero, Alban Bornet
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. 1914-1924 - Yujie Qian
MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. 1925-1934 - Mehdi Khashei
Intelligent Discrete Deep Learning Based Classification Methodology in Chemometrics. 1935-1946 - Gregory W. Kyro
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction. 1947-1960 - Jiuyang Zhao
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain. 1961-1981 - Ji Ding
Vina-GPU 2.0: Further Accelerating AutoDock Vina and Its Derivatives with Graphics Processing Units. 1982-1998 - Jeronimo F. Silva, Guilherme S. L. Fabris
TopIso3D Viewer: Enhancing Topological Analysis through 3D Isosurfaces. 1999-2013 - Alessandro Nicoli
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. 2014-2029 - Valerie Welborn, William R. Archer
Characterizing Ion-Polymer Interactions in Aqueous Environment with Electric Fields. 2030-2036 - Yu Zhao, Menglu Cui, Yongkang Lyu, Wen Gao, Xixi Cui, Changzhe Zhang, Qingtian Meng
External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C+:C Base Pair. 2037-2046 - Werner Treptow
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands. 2047-2057 - Arup Mondal
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations. 2058-2072 - Goutam Mukherjee
Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design. 2073-2083 - Metehan Ilter
Structural Dynamics of Lys11-Selective Deubiquitinylase Cezanne-1 during the Catalytic Cycle. 2084-2094 - Bidhya Thapa, Narayan P. Adhikari
A 5′-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. 2095-2103 - Nopawit Khamto, Kraikrit Utama
Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CLPro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity. 2104-2121 - Rajdip Misra
Loop Dynamics and Conformational Flexibility in Dengue Serine Protease Activity: Noninvasive Perturbation by Solvent Exchange. 2122-2132 - Petra Kührová
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. 2133-2146 - Mateusz Marcisz, Sergey A. Samsonov
Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. 2147-2157 - Olivia Garland
Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. 2158-2169 - Ernest Awoonor-Williams
Benchmarking In Silico Tools for Cysteine pKa Prediction. 2170-2180 - Ziad Fakhoury
Generating Protein Folding Trajectories Using Contact-Map-Driven Directed Walks. 2181-2195 - Paween Mahinthichaichan
Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis. 2196-2206 - Samiran Sen
Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble. 2207-2217 - Christian Kersten
Hic Sunt Dracones: Molecular Docking in Uncharted Territories with Structures from AlphaFold2 and RoseTTAfold. 2218-2225 - Folorunsho Bright Omage
Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro). 2226-2239 - Jianan Li
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. 2240-2250 - Kailong Li, Lijun Quan
Simultaneous Prediction of Interaction Sites on the Protein and Peptide Sides of Complexes through Multilayer Graph Convolutional Networks. 2251-2262 - Yang Zhou
Correction to "Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4". 2263-2264 - Patrick Bleiziffer, Kay Schaller
Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". 2265 - Derek van Tilborg, Alisa Alenicheva, Francesca Grisoni
Correction to "Exposing the Limitations of Molecular Machine Learning with Activity Cliffs". 2266
Volume 63, Number 8, April 2023
- Claudio N. Cavasotto
The Impact of Supervised Learning Methods in Ultralarge High-Throughput Docking. 2267-2280 - Yoona Yang
Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces. 2281-2295 - Parisa Mollaei, Amir Barati Farimani
Activity Map and Transition Pathways of G Protein-Coupled Receptor Revealed by Machine Learning. 2296-2304 - Labeeb Ali
Prediction of Thermogravimetric Data in Bromine Captured from Brominated Flame Retardants (BFRs) in e-Waste Treatment Using Machine Learning Approaches. 2305-2320 - Tuan Xu, Shuaizhang Li, Andrew J. Li
Identification of Potent and Selective Acetylcholinesterase/Butyrylcholinesterase Inhibitors by Virtual Screening. 2321-2330 - Meenakshi Verma
Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins. 2331-2344 - Yanqing Duan
Improved GNNs for Log D7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. 2345-2359 - Francois Berenger
3D-Sensitive Encoding of Pharmacophore Features. 2360-2369 - Robert M. Raddi
BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations. 2370-2381 - Dahlia R. Weiss
On Ternary Complex Stability in Protein Degradation: In Silico Molecular Glue Binding Affinity Calculations. 2382-2392 - Suvankar Ghosh
Bridging Thermodynamics, Antimicrobial Activity, and pH Sensitivity of Cationic Membranolytic Heptapeptides-A Computational and Experimental Study. 2393-2408 - Xue-Li Hao, Ai-Min Ren
Theoretical Studies and Design Strategies of Highly Efficient Two-Photon Excited Fluorescent Probes for Hydrogen Sulfide Detection through Simulation of Excited-State Dynamics. 2409-2418 - Phu K. Tang, Prabir Khatua, Vincenzo Carnevale
Exploration of the Nucleation Pathway for Supramolecular Fibers. 2419-2426 - Rohan Yuri Sanspeur
WhereWulff: A Semiautonomous Workflow for Systematic Catalyst Surface Reactivity under Reaction Conditions. 2427-2437 - Francesc Sabanés Zariquiey
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. 2438-2444 - Kira R. Mills
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter. 2445-2455 - Xiaoyue Ji, Xiaochen Cui, Zhengxin Li, Taeyoung Choi, Ying Wang, Wen Xiao, Yunshuo Zhao, Jinyin Zha, Jian Zhang
Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model. 2456-2468 - Anupam Anand Ojha
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. 2469-2482 - Aarion Romany
Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases. 2483-2494 - Cristina González Fernández
Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An In Silico Study through MD Simulations. 2495-2504 - Lauren Winkler
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. 2505-2511 - Haohao Fu
Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling. 2512-2519 - Ernest Awoonor-Williams
Leveraging Advanced In Silico Techniques in Early Drug Discovery: A Study of Potent Small-Molecule YAP-TEAD PPI Disruptors. 2520-2531 - Zahra Ghorbanali
DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs. 2532-2545 - Mehrad Ansari, Andrew D. White
Serverless Prediction of Peptide Properties with Recurrent Neural Networks. 2546-2553 - Afra Sabei
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. 2554-2572 - Torben Gutermuth
Modeling with Alternate Locations in X-ray Protein Structures. 2573-2585 - Barbara Scalvini
Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins. 2586-2602
Volume 63, Number 9, May 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Harvinder Singh
Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study. 2603-2608 - Camila M. Clemente
Best Practices on QM/MM Simulations of Biological Systems. 2609-2627 - Thi Tuyet Van Tran
Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives. 2628-2643 - Jack B. Greisman
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. 2644-2650 - Felix Teufel
Deorphanizing Peptides Using Structure Prediction. 2651-2655 - Edison Mucllari, Vasily Zadorozhnyy, Qiang Ye, Duc Duy Nguyen
Novel Molecular Representations Using Neumann-Cayley Orthogonal Gated Recurrent Unit. 2656-2666 - David Buterez
MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning. 2667-2678 - Gao-Peng Ren
Enhancing Molecular Representations Via Graph Transformation Layers. 2679-2688 - Maria J. Falaguera
Illuminating the Chemical Space of Untargeted Proteins. 2689-2698 - Stuart J. McElhany, Thomas J. Summers
Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions. 2699-2706 - Bundit Kamsri
Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity. 2707-2718 - Kirill Shmilovich
DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries. 2719-2727 - Farzad Molani
Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy. 2728-2734 - Benjamin I. Tingle, John J. Irwin
Large-Scale Docking in the Cloud. 2735-2741 - Xinyu Xia
Determining Reaction Paths by Evaluating Kinetic Isotopic Effects with Density Functional Theory: Example of Methane Thermogenesis. 2742-2747 - Matthew C. Chan
The Effects of N-Linked Glycosylation on SLC6 Transporters. 2748-2758 - Xue Zhang, Xinyi Li, Yijing Wang, Xianghui Zhang
Computational Study of the Fe(II) and α-Ketoglutarate-Dependent Aryloxyalkanoate Dioxygenase (AAD-1) in the Degradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid. 2759-2768 - Moses K. J. Chung
Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. 2769-2782 - Irfan Muhammad
Exploration of the Interaction of Cadmium and Aptamer by Molecular Simulation and Development of Sensitive Capillary Zone Electrophoresis-Based Aptasensor. 2783-2793 - Zhengyue Zhang
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. 2794-2809 - João Morado
Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. 2810-2827 - Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn
Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. 2828-2841 - Francesca Galvani
Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations. 2842-2856 - Sridip Parui
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. 2857-2865 - Luiz Carlos Saramago
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro. 2866-2880 - Moran Zhou, Jiamin Sun, Zhuohang Yu, Zengrui Wu, Weihua Li
Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods. 2881-2894
Volume 63, Number 10, May 2023
- Samuel Boobier
AI4Green: An Open-Source ELN for Green and Sustainable Chemistry. 2895-2901 - Steffen Wolf
Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges. 2902-2910 - Mercedes Alfonso-Prieto
Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. 2911-2917 - Chien-Ting Kao
Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design. 2918-2927 - Hou Yee Choo, Junjie Wee
Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery. 2928-2935 - Zhitao Cai, Tengzi Liu, Qiaoling Lin, Jiahao He, Xiaowei Lei, Fangfang Luo, Yandong Huang
Basis for Accurate Protein pKa Prediction with Machine Learning. 2936-2947 - Xiang-Wei Zhu
Building Machine Learning Small Molecule Melting Points and Solubility Models Using CCDC Melting Points Dataset. 2948-2959 - Jyotsnamayee Nayak, Ashita Sood, Mahesh Kulharia, Suban K. Sahoo, Rajender Kumar
Structural Distortion of β-Cyclodextrin Plays a Key Role in the pH-dependent Host-Guest Chemistry with Doxorubicin, Evident by the Electrochemical and Molecular Dynamics Approach. 2975-2982 - Evrim Arslan, Zeynep Pinar Haslak
Quantum Mechanical Prediction of Dissociation Constants for Thiazol-2-imine Derivatives. 2992-3004 - Rong Yang, Linhua Liu
Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology. 3005-3017 - Lijun Lang, Antonio Frontera
Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work. 3018-3029 - Karoline Sanches
Interaction of the Inhibitory Peptides ShK and HmK with the Voltage-Gated Potassium Channel KV1.3: Role of Conformational Dynamics. 3043-3053 - Amrutha Keshavamurthy
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein. 3054-3067 - Evan J. van Aalst, Corey J. McDonald, Benjamin J. Wylie
Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study. 3068-3085 - Riccardo Rozza
Monovalent Ionic Atmosphere Modulates the Selection of Suboptimal RNA Sequences by Splicing Factors' RNA Recognition Motifs. 3086-3093 - Almotasem Belah Alhamwi
Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein 3 Complex of Haemophilus influenzae. 3094-3104 - Jon Uranga
The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis. 3118-3127 - Joel Graef
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. 3128-3137 - Lucija Hok
Selective Deuteration Improves the Affinity of Adenosine A2A Receptor Ligands: A Computational Case Study with Istradefylline and Caffeine. 3138-3149 - Rameshwar L. Kumawat
High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. 3150-3157 - Erik Endres
MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case. 3186-3197 - Robert Fraczkiewicz
pK50─A Rigorous Indicator of Individual Functional Group Acidity/Basicity in Multiprotic Compounds. 3198-3208 - Javier Vázquez
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits. 3209-3225 - Jack Scantlebury
A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening. 2960-2974 - Yuwei Yang
Deep Generation Model Guided by the Docking Score for Active Molecular Design. 2983-2991 - Crescenzo Coppa
Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models. 3030-3042 - Jacqueline C. Calderón
General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. 3105-3117 - Sudhanshu Shanker
Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking. 3158-3170 - Wei Chen, Di Cui, Steven V. Jerome
Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations. 3171-3185
Volume 63, Number 11, June 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Thereza A. Soares
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. 3227-3229 - Yong Xiao Yang
AREA-AFFINITY: A Web Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities. 3230-3237 - Tobiasz Cieplinski, Tomasz Danel
Generative Models Should at Least Be Able to Design Molecules That Dock Well: A New Benchmark. 3238-3247 - Shayma El-Atawneh
Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes. 3248-3262 - Cheng Fang
Prospective Validation of Machine Learning Algorithms for Absorption, Distribution, Metabolism, and Excretion Prediction: An Industrial Perspective. 3263-3274 - Hossein Hajiabolhassan
FunQG: Molecular Representation Learning via Quotient Graphs. 3275-3287 - Yiwen Lu, Dilek Yalcin
Interpretable Machine Learning Models for Phase Prediction in Polymerization-Induced Self-Assembly. 3288-3306 - Po-Yu Kao
Exploring the Advantages of Quantum Generative Adversarial Networks in Generative Chemistry. 3307-3318 - Jike Wang, Yundian Zeng
Molecular Generation with Reduced Labeling through Constraint Architecture. 3319-3327 - Arun K. Rathod
Phase Transition and Phase Separation in Realistic Thylakoid Lipid Membrane of Marine Algae in All-Atom Simulations. 3328-3339 - Mario Öeren
Predicting Regioselectivity of Cytosolic Sulfotransferase Metabolism for Drugs. 3340-3349 - Xu Qian, Xiaowen Dai
An Interpretable Multitask Framework BiLAT Enables Accurate Prediction of Cyclin-Dependent Protein Kinase Inhibitors. 3350-3368 - Shinji Iida
Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation. 3369-3376 - Bharat Medasani
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. 3377-3391 - Jan P. Unsleber
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application. 3392-3403 - Pabitra Narayan Samanta
Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism. 3404-3422 - Stephanie Wills
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search. 3423-3437 - Darren J. Hsu
tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking. 3438-3447 - Bart M. H. Bruininks
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries. 3448-3452 - Adekunle Aina
PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles. 3453-3461 - Eric R. Hantz
Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. 3462-3473 - Bin Sun
Synergistic Binding of ATP and Nucleic Acids Necessitates UPF1's ATPase Functional Cycle. 3474-3485 - Martin Ljubic
All-Atom Simulations Reveal the Intricacies of Signal Transduction upon Binding of the HLA-E Ligand to the Transmembrane Inhibitory CD94/NKG2A Receptor. 3486-3499 - Niu Zhang, Zhicheng Zuo
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition. 3500-3509 - Felipe Curtolo
Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. 3510-3520 - Joseph Clayton
Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease. 3521-3533 - Austin M. Cool, Steffen Lindert
Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. 3534-3543 - Guillem Vila-Julià
A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics. 3544-3556 - Samuel Cajahuaringa
MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. 3557-3566 - Ying Wang, Jia Xu, Fengjuan Huang, Jiajia Yan, Xinjie Fan, Yu Zou
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges. 3567-3578 - Fangying Li, Yujie Chen
Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift. 3579-3590 - Fengjuan Huang, Ying Wang, Yu Zhang, Chuang Wang
Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein. 3591-3600 - Francesca Alessandra Ambrosio
Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach. 3601-3613 - Yadi Xu
Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein-Protein Interaction. 3614-3627
Volume 63, Number 12, June 2023
- Martin Sícho
DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. 3629-3636 - Maria Bzówka
Recent Advances in Studying Toll-like Receptors with the Use of Computational Methods. 3669-3687 - Dizhou Wu, Freddie R. Salsbury Jr.
Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. 3705-3718 - Jonas Elsborg
Equivariant Graph-Representation-Based Actor-Critic Reinforcement Learning for Nanoparticle Design. 3731-3741 - Yanfei Guan
SNAr Regioselectivity Predictions: Machine Learning Triggering DFT Reaction Modeling through Statistical Threshold. 3751-3760 - João Victor da Silva Guerra
Cavity Characterization in Supramolecular Cages. 3772-3785 - Morgan Lawrenz, Mats Svensson, Mitsunori Kato, Karen H. Dingley, Jackson Chief Elk, Zhe Nie, Yefen Zou, Zachary Kaplan
A Computational Physics-based Approach to Predict Unbound Brain-to-Plasma Partition Coefficient, Kp,uu. 3786-3798 - András F. Wacha
Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association. 3799-3813 - Charly Empereur-mot
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. 3827-3838 - Michael Souffrant, Xin-Qiu Yao
Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance. 3892-3902 - Yueying Yang, Yang Liu, Kuiru Sa, Hui Wang, Yu Lin, Hua Li
Structure-Based Drug Design and Synthesis of Pyrrolidine-2,5-diones as Novel TNF-α Inhibitors. 3911-3924 - Ute F. Röhrig
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking. 3925-3940 - Marc Graille
Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology. 3637-3646 - Bharath Raghavan
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations. 3647-3658 - Eunjae Shim
Machine Learning Strategies for Reaction Development: Toward the Low-Data Limit. 3659-3668 - Sohvi Luukkonen, Erik Meijer
Large-Scale Modeling of Sparse Protein Kinase Activity Data. 3688-3696 - Angela Medvedeva, Hamid Teimouri, Anatoly B. Kolomeisky
Predicting Antimicrobial Activity for Untested Peptide-Based Drugs Using Collaborative Filtering and Link Prediction. 3697-3704 - Wenyi Zhang, Kaiyue Zhang, Jing Huang
A Simple Way to Incorporate Target Structural Information in Molecular Generative Models. 3719-3730 - Chunhui Li
Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning. 3742-3750 - Alejandro Santana-Bonilla, Raquel Lopez-Rios de Castro
Modular Software for Generating and Modeling Diverse Polymer Databases. 3761-3771 - Qinyang Li, Rongzhi Dong, Nihang Fu, Sadman Sadeed Omee
Global Mapping of Structures and Properties of Crystal Materials. 3814-3826 - Burcu Ozden, Ramachandran Boopathi
Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox. 3839-3853 - Kuan Liang, Wanqian Dong, Jiamin Gao, Zhenhao Liu, Rui Zhou, Zhengyu Shu, Mojie Duan:
The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water-Oil Interfaces. 3854-3864 - Natalie Petrillo, Kim Dinh, Kimberly A. Vogt, Shuhua Ma
Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations. 3865-3877 - Ioana M. Ilie
Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. 3878-3891 - Thanapon Charoenwongpaiboon
Mechanistic Insights into Roseoflavin Synthesis by N,N-8-Demethyl-8-aminoriboflavin Dimethyltransferase (RosA): Molecular Dynamics Simulations and Residue Conservation Analysis. 3903-3910 - Lianlian Wu, Xiaona Ye, Yixin Zhang, Jie Gao, Zhikai Lin, Binsheng Sui, Yuqi Wen, Qingqiang Wu, Kunhong Liu, Song He
A Genetic Algorithm-Based Ensemble Learning Framework for Drug Combination Prediction. 3941-3954 - Lei Deng, Ying Jiang
ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction. 3955-3966 - Xiangzhen Zan, Ranze Xie, Xiangyu Yao, Peng Xu, Wenbin Liu
A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding. 3967-3976
Volume 63, Number 13, July 2023
- Salvatore Galati
MolBook UNIPI─Create, Manage, Analyze, and Share Your Chemical Data for Free. 3977-3982 - Philippe Gendreau, Joseph-André Turk, Nicolas Drizard, Vinicius Barros Ribeiro da Silva
Molecular Assays Simulator to Unravel Predictors Hacking in Goal-Directed Molecular Generations. 3983-3998 - Nutaya Pravalphruekul
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder. 3999-4011 - Esther Heid
Characterizing Uncertainty in Machine Learning for Chemistry. 4012-4029 - Yujie Qian
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. 4030-4041 - Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath
Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case. 4042-4055 - Juliana Castro-Amorim
Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? 4056-4069 - Serah W. Kimani, Julie Owen, Stuart R. Green
Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets. 4070-4078 - Eric Fagerberg
Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining. 4079-4087 - Toshifumi Yui
Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase. 4088-4099 - Miguel Gallegos
Developing a User-Friendly Code for the Fast Estimation of Well-Behaved Real-Space Partial Charges. 4100-4114 - Christine Y. Yeh
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. 4115-4124 - Mitchell Benton, Mercede Furr, Vivek Govind Kumar
cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach. 4125-4137 - Débora Bublitz Anton
Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2. 4138-4146 - Zhenhao Liu
Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding. 4147-4157 - Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu
Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features. 4158-4169 - Renqing Zeng, Longxue Cai, Jose Manuel Perez-Aguilar
Robust Mechanical Destruction to the Cell Membrane of Carbon Nitride Polyaniline (C3N): A Molecular Dynamics Simulation Study. 4170-4179 - Sefora Naomi Agrò
Molecular Dynamics Simulations Elucidate the Molecular Basis of Pre-mRNA Translocation by the Prp2 Spliceosomal Helicase. 4180-4189 - Yazdan Maghsoud
Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study. 4190-4206 - Song Li
LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty. 4207-4215 - Jialin Bi
Multiscale Topological Indices for the Quantitative Prediction of SARS CoV-2 Binding Affinity Change upon Mutations. 4216-4227 - Meenakshi Verma, Laxmikant Trivedi, Prema G. Vasudev:
Correction to "Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins". 4228
Volume 63, Number 14, July 2023
- Daniel R. Bryan, John L. Kulp Jr., Manoj K. Mahapatra
BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. 4229-4236 - Valentina Sora, Matteo Tiberti
PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. 4237-4245 - András F. Wacha
charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS. 4246-4252 - Rocío Mercado
Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. 4253-4265 - Stanley Lo
Augmenting Polymer Datasets by Iterative Rearrangement. 4266-4276 - Xiaowei Shen
A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction. 4277-4290 - Keshavan Seshadri
Molecular Dynamics and Machine Learning Study of Adrenaline Dynamics in the Binding Pocket of GPCR. 4291-4300 - Lulu Zheng, Bin Zhu
Pharmaceutical Cocrystal Discovery via 3D-SMINBR: A New Network Recommendation Tool Augmented by 3D Molecular Conformations. 4301-4311 - Fabio Falcioni
How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach. 4312-4327 - Subhamoy Mahajan
Automated Parameterization of Coarse-Grained Polyethylenimine under a Martini Framework. 4328-4341 - Siddhant M. Lambor, Sashank Kasiraju
CKineticsDB─An Extensible and FAIR Data Management Framework and Datahub for Multiscale Modeling in Heterogeneous Catalysis. 4342-4354 - Yupeng Huang
DSDP: A Blind Docking Strategy Accelerated by GPUs. 4355-4363 - Ching Ching Lam
CONFPASS: Fast DFT Re-Optimizations of Structures from Conformation Searches. 4364-4375 - Son Tung Ngo
Morphology of a Transmembrane Aβ42 Tetramer via REMD Simulations. 4376-4382 - Ronen Zangi
Multimerizations, Aggregation, and Transfer Reactions of Small Numbers of Molecules. 4383-4391 - Wei-Bo Cui, Xue Wei, Jing-Fu Guo, Xue-Li Hao, Lu-Yi Zou, Song Wang, Hui Li
Molecular Design of Highly Efficient Heavy-Atom-free NpImidazole Derivatives for Two-Photon Photodynamic Therapy and ClO- Detection. 4392-4404 - Tareq Hameduh
Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs. 4405-4422 - Meina Ren, Ziyi Ma, Lina Zhao, Yanjiao Wang, Hailong An
Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection. 4423-4432 - Tomás F. D. Silva
Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides. 4433-4446 - Nuno F. B. Oliveira
Interfacial Dynamics and Growth Modes of β2-Microglobulin Dimers. 4447-4457 - Shengzhe Deng
Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. 4458-4467 - Katsuki Takebe, Mamoru Suzuki, Takao Kuwada-Kusunose, Satoko Shirai, Kaori Fukuzawa
Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses. 4468-4476
Volume 63, Number 15, August 2023
- Emmanuel V. Péan
PEARS: A Web Tool for Fitting Time-Resolved Photoluminescence Decays of Perovskite Materials. 4477-4482 - Trinidad Novoa
The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. 4483-4489 - Jun Liao, Zirui Shu, Junyong Gao, Mincong Wu, Changjun Chen
SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules. 4490-4496 - Jessica Lanini
PREFER: A New Predictive Modeling Framework for Molecular Discovery. 4497-4504 - Alexander Hagg
Open-Source Machine Learning in Computational Chemistry. 4505-4532 - Christophe Chipot
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice? 4533-4544 - Tom Bailey
Gradient Boosted Machine Learning Model to Predict H2, CH4, and CO2 Uptake in Metal-Organic Frameworks Using Experimental Data. 4545-4551 - Takuto Koyama
Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples. 4552-4559 - Jin Da Tan, Balamurugan Ramalingam, Swee Liang Wong, Jayce Jian Wei Cheng
Transfer Learning of Full Molecular Weight Distributions via High-Throughput Computer-Controlled Polymerization. 4560-4573 - Sayandeep Biswas
Predicting Critical Properties and Acentric Factors of Fluids Using Multitask Machine Learning. 4574-4588 - Jonathan Parkinson
Linear-Scaling Kernels for Protein Sequences and Small Molecules Outperform Deep Learning While Providing Uncertainty Quantitation and Improved Interpretability. 4589-4601 - Feyza Kelleci Çelik
Machine Learning-Based Prediction of Drug-Induced Hepatotoxicity: An OvA-QSTR Approach. 4602-4614 - Tianyi Wang
Infrared Spectral Analysis for Prediction of Functional Groups Based on Feature-Aggregated Deep Learning. 4615-4622 - Daniel Platero-Rochart
Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. 4623-4632 - Yan Xiang
Interpretable Molecular Property Predictions Using Marginalized Graph Kernels. 4633-4640 - William K. Weigel, Alba L. Montoya, Raphael M. Franzini
Evaluation of the Topology Space of DNA-Encoded Libraries. 4641-4653 - Jokent T. Gaza
Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study. 4654-4663 - Mariano Spivak
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. 4664-4678 - Bo-Wen Yin
Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations. 4679-4690 - Lucas G. Viviani
Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. 4691-4707 - Xin Wang, Jing Ma, Jianhua Fan, Hui Zhu, Xingman Liu, Hongqiang Xia
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight. 4708-4715 - Petr Stadlbauer
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. 4716-4731 - Samo Lesnik
Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor. 4732-4748 - Yan Li
HydraMap v.2: Prediction of Hydration Sites and Desolvation Energy with Refined Statistical Potentials. 4749-4761 - Xue Zhang, Lei Li, Qingchuan Zheng
Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics. 4762-4771 - Hugo Guterres
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes. 4772-4779 - Haiyan Cai
Discovery of Novel SIRT1/2 Inhibitors with Effective Cytotoxicity against Human Leukemia Cells. 4780-4790 - Christopher Lockhart
Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites? 4791-4802 - Defa Huang, Cong Guo
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation. 4803-4813 - Sarmistha Majumdar, Francesco Di Palma
Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. 4814-4826 - Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Ran Friedman
Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. 4827-4838 - Ebru Çetin
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. 4839-4849 - Jiaqi Liu, Jian Wan
DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein-Ligand Binding Affinity Prediction. 4850-4863 - Amit Kumar
Mechanism of Ligand Discrimination by the NMT1 Riboswitch. 4864-4874 - Deborah Palazzotti, Tommaso Felicetti
Fighting Antimicrobial Resistance: Insights on How the Staphylococcus aureus NorA Efflux Pump Recognizes 2-Phenylquinoline Inhibitors by Supervised Molecular Dynamics (SuMD) and Molecular Docking Simulations. 4875-4887 - Flavio Costa
Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243. 4888-4899 - Christian Wennberg
Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. 4900-4911 - Ruibin Liu
Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads. 4912-4923 - Silvia Gervasoni
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations. 4924-4933 - Shubham Vishnoi
Computational Peptide Design Cotargeting Glucagon and Glucagon-like Peptide-1 Receptors. 4934-4947 - Xinyue Liu, Jinying Liu, Bangze Fu, Ruzhen Chen, Jianzhou Jiang, He Chen, Runa Li, Lin Xing, Liying Yuan, Xuetai Chen, Jing Zhang, Honglei Li, Shuzhen Guo
DCABM-TCM: A Database of Constituents Absorbed into the Blood and Metabolites of Traditional Chinese Medicine. 4948-4959 - Xiao-Wei Liu, Tian-Yu Shi, Dong Gao, Cai-Yi Ma, Hao Lin
iPADD: A Computational Tool for Predicting Potential Antidiabetic Drugs Using Machine Learning Algorithms. 4960-4969 - Ji Lv
Identification of Robust Antibiotic Subgroups by Integrating Multi-Species Drug-Drug Interactions. 4970-4978
Volume 63, Number 16, August 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Henrique M. Cezar
SANS Spectra with PLUMED: Implementation and Application to Metainference. 4979-4985 - Bing He
FFMDFPA: A FAIRification Framework for Materials Data with No-Code Flexible Semi-Structured Parser and Application Programming Interfaces. 4986-4994 - Susanta Das
Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input. 4995-5000 - Kuo-Hao Lee, Jamie J. Manning
A Novel "Activation Switch" Motif Common to All Aminergic Receptors. 5001-5017 - Fan Zhang, Tao Zeng, Ruibo Wu
QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. 5018-5034 - Sherwin S. S. Ng, Yunpeng Lu
Evaluating the Use of Graph Neural Networks and Transfer Learning for Oral Bioavailability Prediction. 5035-5044 - Johnathan von der Heyde, Walter Malone
Combining Deep Learning Neural Networks with Genetic Algorithms to Map Nanocluster Configuration Spaces with Quantum Accuracy at Low Computational Cost. 5045-5055 - Leslie Salas-Estrada, Davide Provasi
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. 5056-5065 - Sarveswara Rao Vangala, Sowmya Ramaswamy Krishnan
pBRICS: A Novel Fragmentation Method for Explainable Property Prediction of Drug-Like Small Molecules. 5066-5076 - Krittapong Deshsorn
Unlocking the Full Potential of Heteroatom-Doped Graphene-Based Supercapacitors through Stacking Models and SHAP-Guided Optimization. 5077-5088 - Jiacheng Ma, Zhenya Du
Intermolecular 3D-MoRSE Descriptors for Fast and Accurate Prediction of Electronic Couplings in Organic Semiconductors. 5089-5096 - Yu Zhang, Jinhui Yu, Hongwei Song
Structure-Based Reaction Descriptors for Predicting Rate Constants by Machine Learning: Application to Hydrogen Abstraction from Alkanes by CH3/H/O Radicals. 5097-5106 - Giuseppe Lamanna
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. 5107-5119 - Chris Zhang
Building Block-Based Binding Predictions for DNA-Encoded Libraries. 5120-5132 - Thomas Liphardt
Fast Substructure Search in Combinatorial Library Spaces. 5133-5141 - Nara Lee Chon, Natalie Jean Schultz, Hongjin Zheng, Hai Lin
Anion Pathways in the NarK Nitrate/Nitrite Exchanger. 5142-5152 - Matthew S. Johnson
Pynta─An Automated Workflow for Calculation of Surface and Gas-Surface Kinetics. 5153-5168 - Wanlei Wei
Comparative Performance of High-Throughput Methods for Protein pKa Predictions. 5169-5181 - Shubhandra Tripathi, Nisanth N. Nair
Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein. 5182-5191 - Shubhashree Barik
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations. 5192-5203 - Vid Ravnik
Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. 5204-5219 - Florent Barbault
DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. 5220-5231 - Haiyi Chen, Yue Guo, Shengqing Ye
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. 5232-5243 - Piyatida Pojtanadithee, Kowit Hengphasatporn
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches. 5244-5258 - Federica Battistini
Sequence-Dependent Properties of the RNA Duplex. 5259-5271 - Sian Xiao
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. 5272-5296 - Jianwen Zhang, Yalong Cong
Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation. 5297-5308 - Mohammad Mehdi Ghahremanpour
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. 5309-5318 - Jeremy Lapierre
Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy. 5319-5330 - Luz América Chi-Uluac
Atomistic Molecular Insights into Angiotensin-(1-7) Interpeptide Interactions. 5331-5340 - Lin Wei
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study. 5341-5355 - Justin Carbone
Inhibition Mechanism of Anti-TB Drug SQ109: Allosteric Inhibition of TMM Translocation of Mycobacterium Tuberculosis MmpL3 Transporter. 5356-5374 - Nitin Kumar Singh
Hydrophobicity─A Single Parameter for the Accurate Prediction of Disordered Regions in Proteins. 5375-5383 - Meng-Meng Wei
BCMCMI: A Fusion Model for Predicting circRNA-miRNA Interactions Combining Semantic and Meta-path. 5384-5394
Volume 63, Number 17, September 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr.
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. 5395 - Mark A. Watson, Ryne C. Johnston
Comment on the Definition and Labeling of pK50. 5396-5399 - R. A. Talmazan, Maren Podewitz
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent. 5400-5407 - Barmak Mostofian
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. 5408-5432 - Olivier J. M. Béquignon
Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. 5433-5445 - Luis Cesar de Azevedo
Effect of Flattened Structures of Molecules and Materials on Machine Learning Model Training. 5446-5456 - Changchang Liu
A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. 5457-5472 - Han Zhang
Property Prediction and Structural Feature Extraction of Polyimide Materials Based on Machine Learning. 5473-5483 - Mario Latendresse
SynRoute: A Retrosynthetic Planning Software. 5484-5495 - Loriano Storchi
DeepGRID: Deep Learning Using GRID Descriptors for BBB Prediction. 5496-5512 - Moayad Alnammi, Shengchao Liu, Spencer S. Ericksen
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries. 5513-5528 - Srishyam Raghavan, Brian P. Chaplin
Small-Molecule Adsorption Energy Predictions for High-Throughput Screening of Electrocatalysts. 5529-5538 - Mitsuru Ohno
SMiPoly: Generation of a Synthesizable Polymer Virtual Library Using Rule-Based Polymerization Reactions. 5539-5548 - Thomas Seidel
High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment. 5549-5570 - Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath
Meta-GTM: Visualization and Analysis of the Chemical Library Space. 5571-5582 - Abhik Ghosh Moulick
Fluctuation-Dominated Ligand Binding in Molten Globule Protein. 5583-5591 - Cesar de Oliveira
FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning. 5592-5603 - Vladimír Sládek
How E-, L-, and P-Selectins Bind to sLex and PSGL-1: A Quantification of Critical Residue Interactions. 5604-5618 - Ghazi A. Al Jabal
In Silico Prediction and Biophysical Validation of Novel 14-3-3σ Homodimer Stabilizers. 5619-5630 - Giulia Bianco, Matthew Holcomb
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. 5631-5640 - Rafael Giordano Viegas
Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. 5641-5649 - Qianzhen Shao
EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. 5650-5659 - Shakuntala Dhurua, Madhurima Jana
Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation. 5660-5675 - Milorad Andjelkovic
Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations. 5676-5688 - Jun Hu
Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism. 5689-5700
Volume 63, Number 18, September 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Raimondas Galvelis
NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. 5701-5708 - Susanne Sauer
Integrating Reaction Schemes, Reagent Databases, and Virtual Libraries into Fragment-Based Design by Reinforcement Learning. 5709-5726 - Ryann Perez, Xinning Li, Sam Giannakoulias
AggBERT: Best in Class Prediction of Hexapeptide Amyloidogenesis with a Semi-Supervised ProtBERT Model. 5727-5733 - Maho Nakata
PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations. 5734-5754 - Seunghee Han
Design of New Inorganic Crystals with the Desired Composition Using Deep Learning. 5755-5763 - Kohei Motojima, Abhijit Sen
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions. 5764-5772 - Toni Sivula
Machine Learning-Boosted Docking Enables the Efficient Structure-Based Virtual Screening of Giga-Scale Enumerated Chemical Libraries. 5773-5783 - Nicholas B. Smith
Comparison of Taboo Search Methods for Atomic Cluster Global Optimization with a Basin-Hopping Algorithm. 5784-5793 - Simon Axelrod
Mapping the Space of Photoswitchable Ligands and Photodruggable Proteins with Computational Modeling. 5794-5802 - Guilherme Duarte Ramos Matos
Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. 5803-5822 - Suvankar Ghosh
Effect of Spacer Length Modification of the Cationic Side Chain on the Energetics of Antimicrobial Peptide Binding to Membrane-Mimetic Bilayers. 5823-5833 - Daipayan Sarkar
Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. 5834-5846 - Zhixiang Wu
Dynamic Insights into the Self-Activation Pathway and Allosteric Regulation of the Orphan G-Protein-Coupled Receptor GPR52. 5847-5862 - Gangtong Huang, Huayuan Tang, Yuying Liu, Chi Zhang, Pu Chun Ke
Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. 5863-5873 - Irina D. Pogozheva
Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. 5874-5895 - Zhiyuan Zhao, Jintong Du, Yu Du, Yuan Gao, Mingxuan Yu, Yingkai Zhang
Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations. 5896-5902 - Poonam Pandey, Alexander D. MacKerell Jr.
Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. 5903-5915 - Nicola Gambacorta, Fulvio Ciriaco
CIRCE: Web-Based Platform for the Prediction of Cannabinoid Receptor Ligands Using Explainable Machine Learning. 5916-5926 - Claudia Llinas del Torrent, Iu Raïch, Angel Gonzalez
The Leu/Val6.51 Side Chain of Cannabinoid Receptors Regulates the Binding Mode of the Alkyl Chain of Δ9-Tetrahydrocannabinol. 5927-5935 - Xiaowen Hu
HGCLMDA: Predicting mRNA-Drug Sensitivity Associations via Hypergraph Contrastive Learning. 5936-5946
Volume 63, Number 19, October 2023
- Ariane Nunes-Alves
AlphaFold2 in Molecular Discovery. 5947-5949 - Lawson T. Glasby, Rama Oktavian
Augmented Reality for Enhanced Visualization of MOF Adsorbents. 5950-5955 - Yingchao Yan, Yang Zhao, Huifeng Yao, Jie Feng
RPBP: Deep Retrosynthesis Reaction Prediction Based on Byproducts. 5956-5970 - Zhilong Liang
Automatically Predicting Material Properties with Microscopic Images: Polymer Miscibility as an Example. 5971-5980 - Juhwan Noh
Data-Driven Prediction of Configurational Stability of Molecule-Adsorbed Heterogeneous Catalysts. 5981-5995 - Nicholas T. Runcie, Antonia S. J. S. Mey
SILVR: Guided Diffusion for Molecule Generation. 5996-6005 - Daniel J. Hutton, Kari E. Cordes, Carine Michel
Machine Learning-Based Prediction of Activation Energies for Chemical Reactions on Metal Surfaces. 6006-6013 - Marc Lehner
DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. 6014-6028 - Yingying Ma, Minjie Li
Accelerated Design for High-Entropy Alloys Based on Machine Learning and Multiobjective Optimization. 6029-6042 - Kong Meng, Chenyu Huang, Yaxin Wang, Yunjiang Zhang, Shuyuan Li, Zhaolin Fang, Huimin Wang, Shihao Wei, Shaorui Sun
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction. 6043-6052 - Damian M. Wilary, Jacqueline M. Cole
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes. 6053-6067 - Kevin M. Lefrancois-Gagnon
Toward Universal Substituent Constants: Relating QTAIM Functional Group Descriptors to Substituent Effect Proxies. 6068-6080 - Ali Hashemi
HiREX: High-Throughput Reactivity Exploration for Extended Databases of Transition-Metal Catalysts. 6081-6094 - Süleyman Selim Çinaroglu
Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. 6095-6108 - Diship Srivastava
Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation. 6109-6117 - Zhiyong Guo, Lei Wang, Deming Rao, Weiqiong Liu, Miaomiao Xue, Qisheng Fu, Mengwei Lu, Lingqia Su, Sheng Chen, Binju Wang
Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77. 6118-6128 - Tobias M. Prass
Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations. 6129-6140 - Eduardo R. Almeida
Translocation Processes of Pt(II)-Based Drugs through Human Breast Cancer Cell Membrane: In Silico Experiments. 6141-6155 - Ushashi Banerjee, Adithya Chedere
PathTracer Comprehensively Identifies Hypoxia-Induced Dormancy Adaptations in Mycobacterium tuberculosis. 6156-6167
Volume 63, Number 20, October 2023
- Xiaodan Yin
CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. 6169-6176 - Kornel Ozvoldik
YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities. 6177-6182 - David A. Case
AmberTools. 6183-6191 - Rajesh K. Raju
Cluster-MLP: An Active Learning Genetic Algorithm Framework for Accelerated Discovery of Global Minimum Configurations of Pure and Alloyed Nanoclusters. 6192-6197 - Thi Tuyet Van Tran, Hilal Tayara
Recent Studies of Artificial Intelligence on In Silico Drug Absorption. 6198-6211 - Romain Botella
Swarm Smart Meta-Estimator for 2D/2D Heterostructure Design. 6212-6223 - Fathoni A. Musyaffa, Kirsten Rapp, Holger Gohlke
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW. 6224-6238 - Ye Buehler
Expanding Bioactive Fragment Space with the Generated Database GDB-13s. 6239-6248 - Shuyuan Li, Yunjiang Zhang, Zhaolin Fang, Kong Meng, Rui Tian, Hong He
Extracting the Synthetic Route of Pd-Based Catalysts in Methanol Steam Reforming from the Scientific Literature. 6249-6260 - Kushagra Kashyap, Pinaki Prasad Mahapatra, Shakil Ahmed, Erdem Buyukbingol, Mohammad Imran Siddiqi
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening. 6261-6282 - Sergei F. Vyboishchikov
Dense Neural Network for Calculating Solvation Free Energies from Electronegativity-Equalization Atomic Charges. 6283-6292 - Mark A. Hix, Alice R. Walker
AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations. 6293-6301 - Vincenzo Maria D'amore, Greta Donati, Elena Lenci
Molecular View on the iRGD Peptide Binding Mechanism: Implications for Integrin Activity and Selectivity Profiles. 6302-6315 - Zezheng Yang
Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions. 6316-6331 - Jacqueline C. Calderón
Activation/Deactivation Free-Energy Profiles for the β2-Adrenergic Receptor: Ligand Modes of Action. 6332-6343 - Raphael V. R. Dias, Renan P. Pedro
Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. 6344-6353 - João T. S. Coimbra
Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. 6354-6365 - Hyeonjun Kim
Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA. 6366-6375 - Fengjuan Huang, Xinjie Fan, Ying Wang, Chuang Wang
Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations. 6376-6385 - M. Andrés Velasco-Saavedra
Molecular Insights into the Covalent Binding of Zoxamide to the β-Tubulin of Botrytis cinerea. 6386-6395 - Mark James Horgan, Lukas Zell, Bianka Siewert
Identification of Novel β-Tubulin Inhibitors Using a Combined In Silico/In Vitro Approach. 6396-6411 - Patricia Gómez-Gutiérrez
Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening. 6412-6422 - Zhangyang Chen, Xingqing Xiao
Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy. 6423-6435 - Yasaman Karami
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. 6436-6450 - Hai-Tao Zhu, Yuhao Xia, Gui-Jun Zhang
E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning. 6451-6461
Volume 63, Number 21, November 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Anton S. Kolodnitsky
HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database. 6463-6468 - Marine Bugnon
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization. 6469-6475 - Amandeep Singh Bhatia
Quantum Machine Learning Predicting ADME-Tox Properties in Drug Discovery. 6476-6486 - Muhammad Yasir, Jinyoung Park, Eun-Taek Han, Won Sun Park, Jin-Hee Han, Yong-Soo Kwon, Hee-Jae Lee, Wanjoo Chun
Machine Learning-Based Drug Repositioning of Novel Janus Kinase 2 Inhibitors Utilizing Molecular Docking and Molecular Dynamic Simulation. 6487-6500 - Lan Yu, Xiao He
Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening. 6501-6514 - Yan Xiang
Efficient Exploration of Chemical Compound Space Using Active Learning for Prediction of Thermodynamic Properties of Alkane Molecules. 6515-6524 - Zhe Wang, Haiyang Zhong
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. 6525-6536 - Ali Raza, Jamal Uddin, Abdullah Almuhaimeed
AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional Networks. 6537-6554 - Nathan J. Rebello
BigSMARTS: A Topologically Aware Query Language and Substructure Search Algorithm for Polymer Chemical Structures. 6555-6568 - Laura Pascazio
Chemical Species Ontology for Data Integration and Knowledge Discovery. 6569-6586 - Uschi Dolfus
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. 6587-6597 - Andrew T. McNutt, Fatimah Bisiriyu, Sophia Song, Ananya Vyas, Geoffrey R. Hutchison
Conformer Generation for Structure-Based Drug Design: How Many and How Good? 6598-6607 - Fengyang Han
Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential. 6608-6618 - Kojiro Machi
OSPAR: A Corpus for Extraction of Organic Synthesis Procedures with Argument Roles. 6619-6628 - Dmitry V. Zankov
Multi-Instance Learning Approach to the Modeling of Enantioselectivity of Conformationally Flexible Organic Catalysts. 6629-6641 - Mateo Barria-Urenda
Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. 6642-6654 - Garrett A. Stevenson
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. 6655-6666 - Alessandro Nicoli
Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists. 6667-6680 - Faisal Ahmad, Nousheen Parvaiz, Alexander D. MacKerell Jr.
Non-β Lactam Inhibitors of the Serine β-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi. 6681-6695 - Icaro A. Simon
PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands. 6696-6705 - Leonard Dick
CONAN─Novel Tool to Create and Analyze Liquids in Confined Space. 6706-6716 - Abd. Kakhar Umar
From Linear to Nets: Multiconfiguration Polymer Structure Generation with PolyFlin. 6717-6726 - Wei-Hua Yang, Fang-Qi Yu, Rao Huang
Structural Determination and Hierarchical Evolution of Transition Metal Clusters Based on an Improved Self-Adaptive Differential Evolution with Neighborhood Search Algorithm. 6727-6739 - William Oliveira Soté
In Silico Evaluation of Oligomeric Representations for Molecularly Imprinted Polymer Modeling Using a Biological Template. 6740-6755 - K. Michael Salerno
Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome. 6756-6767 - Yinwei Gu, Yan Li
Probing Conformational Transition of TRPV5 Induced by Mechanical Force Using Coarse-Grained Molecular Dynamics. 6768-6777 - Jason Kurniawan
Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets. 6778-6788 - Samaneh Davoudi
Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes. 6789-6806 - Jorge Enrique Hernández González
Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein-Protein Interfaces Considering Fixed and Variable Protonation States. 6807-6822 - Gilberto Pereira
Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. 6823-6833 - Yazdan Maghsoud
Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. 6834-6850 - Marcelo Depólo Polêto
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. 6851-6862 - Lei Yu
Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. 6863-6876 - Ezequiel N. Frigini
The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. 6877-6889 - Raitis Bobrovs
Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. 6890-6899 - Lorenzo Guidetti
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity. 6900-6911 - Zixuan Cheng, Siaw San Hwang, Mrinal Bhave
Combination of QSAR Modeling and Hybrid-Based Consensus Scoring to Identify Dual-Targeting Inhibitors of PLK1 and p38γ. 6912-6924 - Francini Fonseca Lopez, Jiayuan Miao
Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. 6925-6937 - Xiao Liu
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. 6938-6946 - Shuai Wang
Graph Reasoning Method Based on Affinity Identification and Representation Decoupling for Predicting lncRNA-Disease Associations. 6947-6958
Volume 63, Number 22, November 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Shunzhou Wan
Ensemble-Based Approaches Ensure Reliability and Reproducibility. 6959-6963 - Valentin J. Hoerschinger, Franz Waibl, Nancy D. Pomarici, Johannes R. Loeffler
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. 6964-6971 - Shiru Wu, Xiaowei Yang, Xun Zhao, Zhipu Li, Min Lu
Applications and Advances in Machine Learning Force Fields. 6972-6985 - Arsen Sultanov, Jean-Claude Crivello
Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells. 6986-6997 - Vidushi Sharma
Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance. 6998-7010 - Yanling Wu, Kun Li
Attention Mechanism-Based Graph Neural Network Model for Effective Activity Prediction of SARS-CoV-2 Main Protease Inhibitors: Application to Drug Repurposing as Potential COVID-19 Therapy. 7011-7031 - Tiago Janela, Jürgen Bajorath
Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs. 7032-7044 - Qingyang Dong
Snowball 2.0: Generic Material Data Parser for ChemDataExtractor. 7045-7055 - Ahmad Aakash, Ramsha Kulsoom, Saba Khan, Musab Saeed Siddiqui, Deedar Nabi
Novel Models for Accurate Estimation of Air-Blood Partitioning: Applications to Individual Compounds and Complex Mixtures of Neutral Organic Compounds. 7056-7066 - Mingyuan Xu
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree. 7067-7082 - Manuel A. Llanos
A Combined Ligand- and Structure-Based Virtual Screening To Identify Novel NaV1.2 Blockers: In Vitro Patch Clamp Validation and In Vivo Anticonvulsant Activity. 7083-7096 - Yuliang Shi, Dil K. Limbu
Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks. 7097-7106 - Xuechen Tang, Janik Kokot, Franz Waibl, Monica L. Fernández-Quintero
Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. 7107-7123 - Mirko Paulikat
Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail. 7124-7132 - Candide Champion
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. 7133-7147 - Sebastian Schmitt
Extension of the MolMod Database to Transferable Force Fields. 7148-7158 - Mariah R. Pierce, Jingjing Ji, Sadie X. Novak, Michelle A. Sieburg, Shivangi Nangia, Shikha Nangia
Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization. 7159-7170 - Manuela Maurer
Transmembrane β-Barrel Models of α-Synuclein Oligomers. 7171-7179 - Brandon Havranek
Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach. 7180-7188 - Rui Wang
ChatGPT in Drug Discovery: A Case Study on Anticocaine Addiction Drug Development with Chatbots. 7189-7209 - Anastasia Saar
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. 7210-7218 - Furyal Ahmed
FASTDock: A Pipeline for Allosteric Drug Discovery. 7219-7227 - Lucia Cano-González, Johan D. Espinosa-Mendoza, Félix Matadamas-Martínez, Ariana Romero-Velásquez, Miguel Flores-Ramos
Structure-Based Optimization of Carbendazim-Derived Tubulin Polymerization Inhibitors through Alchemical Free Energy Calculations. 7228-7238 - Fang Ge, Muhammad Arif
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction. 7239-7257 - Jingxin Xie, Lijun Quan
DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features. 7258-7271
Volume 63, Number 23, December 2023
- Kevin J. Naidoo
Modeling Reactions from Chemical Theories to Machine Learning. 7273 - Kristine Degn, Ludovica Beltrame
PDBminer to Find and Annotate Protein Structures for Computational Analysis. 7274-7281 - Luís Queirós-Reis
Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands. 7282-7298 - Melissa Marciesky, Diana S. Aga
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS). 7299-7319 - Zhicheng Zhong, Zeying Li, Jie Yang
Unified Model to Predict gRNA Efficiency across Diverse Cell Lines and CRISPR-Cas9 Systems. 7320-7329 - Jackson W. Burns
QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules. 7330-7337 - Mohammad Mehdi Ghahremanpour
Ensemble Geometric Deep Learning of Aqueous Solubility. 7338-7349 - Evan M. Askenazi
Identification of High-Reliability Regions of Machine Learning Predictions Based on Materials Chemistry. 7350-7362 - Heqi Sun
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions. 7363-7372 - Rui Li, Lin Chen, Xinheng He, Duanhua Cao, Zehong Zhang
Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein. 7373-7381 - Robin Skånberg
VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics. 7382-7391 - Hiroaki Iwata
VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search. 7392-7400 - Dakota L. Folmsbee
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. 7401-7411 - Shu-Sen Chen, Zack Meyer, Brendan Jensen, Alex Kraus, Allison C. Lambert, Daniel H. Ess
ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design. 7412-7422 - Nuno M. S. Almeida
Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex. 7423-7443 - Rupesh Agarwal
Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. 7444-7452 - Miroslava Nedyalkova
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics. 7453-7463 - Andreia Fortuna
Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations. 7464-7475 - Shitong Zhang
Metal-Organic Framework Membrane Constructor: A Tool for High-Throughput Construction of Metal-Organic Framework Membrane Models. 7476-7486 - Xuan Fang
Molecular Insights into the MLCK Activation by CaM. 7487-7498 - Lihua Dong
Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant. 7499-7507 - Riccardo Rozza
Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. 7508-7517 - Luise Jacobsen
Introducing the Automated Ligand Searcher. 7518-7528 - Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou
Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. 7529-7544 - Sudarshan Behera
Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid. 7545-7556 - Minghua Zhao
GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response. 7557-7567 - Shide Liang
Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling. 7568-7577 - Yuko Tsuchiya
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins. 7578-7587 - Rupeng Dai, Xueting Bao, Ying Zhang, Yan Huang, Haohao Zhu
Hot-Spot Residue-Based Virtual Screening of Novel Selective Estrogen-Receptor Degraders for Breast Cancer Treatment. 7588-7602
Volume 63, Number 24, December 2023
- Issue Editorial Masthead.
- Issue Publication Information.
- Giulia Palermo
Editorial: Editing DNA and RNA through Computations. 7603-7604 - Osvaldo N. Oliveira
Artificial Intelligence Agents for Materials Sciences. 7605-7609 - Anthony T. Bogetti
LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways. 7610-7616 - Zhenxing Wu
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. 7617-7627 - Yaguo Gong, Wei Ding, Panpan Wang, Qibiao Wu
Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics. 7628-7641 - Aaron G. Garrison
Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set. 7642-7654 - Zhipeng Wu
Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides. 7655-7668 - Di-Fan Liu, Yong-Xin Zhang
High-Temperature Polymer Dielectrics Designed Using an Invertible Molecular Graph Generative Model. 7669-7675 - Ignacio Pérez-Correa
Transformer-Based Representation of Organic Molecules for Potential Modeling of Physicochemical Properties. 7676-7688 - Pei Zhang
Transferring a Molecular Foundation Model for Polymer Property Predictions. 7689-7698 - Ruixuan Wang, Zhikang Liu, Jiahao Gong, Qingping Zhou
An Uncertainty-Guided Deep Learning Method Facilitates Rapid Screening of CYP3A4 Inhibitors. 7699-7710 - Chen-Hsuan Huang, Shiang-Tai Lin
MARS Plus: An Improved Molecular Design Tool for Complex Compounds Involving Ionic, Stereo, and Cis-Trans Isomeric Structures. 7711-7728 - Rubina, Syed Tarique Moin
Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors. 7729-7743 - Jan Cz. Dobrowolski
HOMA Index Establishes Similarity to a Reference Molecule. 7744-7754 - Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai-Bin Luo, Zhe Li
Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function. 7755-7767 - Genki Kudo
AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. 7768-7777 - Anjana V. Mathath, Bratin Kumar Das, Debashree Chakraborty
Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling. 7778-7790 - Juan José Galano-Frutos
Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. 7791-7806 - Aharon Gomez
Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation. 7807-7815 - Matthijs L. A. Hakkennes
MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes. 7816-7825 - Dongxiao Yue, Hajime Hirao
Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4. 7826-7836 - Huaxin Zhou
Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations. 7837-7846 - Mathilde Goullieux
Two-Step Covalent Docking with Attracting Cavities. 7847-7859 - Naoki Ogawa
Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations. 7860-7872 - Daniel Del Hoyo
Scipion-Chem: An Open Platform for Virtual Drug Screening. 7873-7885 - Jiahui Guan, Lantian Yao
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. 7886-7898
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