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Journal of Cheminformatics, Volume 13
Volume 13, Number 1, December 2021
- Rick Helmus
, Thomas L. ter Laak
patRoon: open source software platform for environmental mass spectrometry based non-target screening. 1 - Maria Sorokina
COCONUT online: Collection of Open Natural Products database. 2 - Ivan Cmelo
Profiling and analysis of chemical compounds using pointwise mutual information. 3 - Umit V. Ucak, Taek Kang
Substructure-based neural machine translation for retrosynthetic prediction. 4 - Kohulan Rajan
Molecule Set Comparator (MSC): a CDK-based open rich-client tool for molecule set similarity evaluations. 5 - Xujun Zhang
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. 6 - Jianwen Chen
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. 7 - Yu-Chieh Huang, Pierre Tremouilhac, An Nguyen, Nicole Jung
ChemSpectra: a web-based spectra editor for analytical data. 8 - Agnieszka Gajewicz-Skretna
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models. 9 - Nicolai Ree, Andreas H. Göller, Jan H. Jensen
RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions. 10 - Beihong Ji
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities. 11 - Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models. 12 - Nicolas Bosc
MAIP: a web service for predicting blood-stage malaria inhibitors. 13 - Andrew E. Blanchard
Using GANs with adaptive training data to search for new molecules. 14 - Márcia Barros
Hybrid semantic recommender system for chemical compounds in large-scale datasets. 15 - Rajarshi Guha
What is the role of cheminformatics in a pandemic? 16 - Leen Kalash
Structure-based identification of dual ligands at the A2AR and PDE10A with anti-proliferative effects in lung cancer cell-lines. 17 - Annachiara Tinivella, Luca Pinzi
Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models. 18 - Emma Schymanski
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag. 19 - Kohulan Rajan
DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature. 20 - Tiago Pereira, Maryam Abbasi
Diversity oriented Deep Reinforcement Learning for targeted molecule generation. 21 - Bingyin Hu
ChemProps: A RESTful API enabled database for composite polymer name standardization. 22 - Janna Hastings
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. 23 - Yongbeom Kwon, Juyong Lee
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES. 24 - Sana Naseem, Yasuyuki Zushi, Deedar Nabi
Development and evaluation of two-parameter linear free energy models for the prediction of human skin permeability coefficient of neutral organic chemicals. 25 - Jiazhen He
Molecular optimization by capturing chemist's intuition using deep neural networks. 26 - Hiroyuki Kuwahara, Xin Gao
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. 27 - Surendra Kumar, Mi-Hyun Kim
SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors. 28 - Amit Kumar Halder, M. Natália Dias Soeiro Cordeiro
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling. 29 - Fan Hu
Multi-PLI: interpretable multi-task deep learning model for unifying protein-ligand interaction datasets. 30 - Manuel Pastor
Flame: an open source framework for model development, hosting, and usage in production environments. 31 - Ramón Alain Miranda-Quintana
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics†. 32 - Ramón Alain Miranda-Quintana
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection. 33 - Kohulan Rajan
STOUT: SMILES to IUPAC names using neural machine translation. 34 - Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth, Andrea Volkamer
Assessing the calibration in toxicological in vitro models with conformal prediction. 35 - Narumi Watanabe, Yuuto Ohnuki, Yasubumi Sakakibara
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. 36 - Bakary N'tji Diallo
SANCDB: an update on South African natural compounds and their readily available analogs. 37 - Jakub Galgonek
IDSM ChemWebRDF: SPARQLing small-molecule datasets. 38 - Morgan C. Thomas
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. 39 - Jonathan M. Goodman
InChI version 1.06: now more than 99.99% reliable. 40 - Mariia Matveieva
Benchmarks for interpretation of QSAR models. 41 - Carl E. Belle
A machine learning platform for the discovery of materials. 42 - Andrew T. McNutt
GNINA 1.0: molecular docking with deep learning. 43 - Faraz Shaikh
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds. 44 - Ondrej Schindler
Optimized SQE atomic charges for peptides accessible via a web application. 45 - Naruki Yoshikawa
Twitter integration of chemistry software tools. 46 - Dea Gogishvili
Nonadditivity in public and inhouse data: implications for drug design. 47 - Mehmet Aziz Yirik
MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle. 48 - Rajarshi Guha
Reply to "FAIR chemical structure in the Journal of Cheminformatics". 49 - Emma Schymanski
FAIR chemical structures in the Journal of Cheminformatics. 50 - Jan Prívratský, Jirí Novák
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis. 51 - Ondrej Schindler
Correction to: Optimized SQE atomic charges for peptides accessible via a web application. 52 - Ruben Pawellek, Jovana Krmar, Adrian Leistner, Nevena Djajic, Biljana Otasevic, Ana Protic, Ulrike Holzgrabe
Charged aerosol detector response modeling for fatty acids based on experimental settings and molecular features: a machine learning approach. 53 - Candida Manelfi, Marica Gemei, Carmine Talarico
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool. 54 - Lea Seep
Ensemble completeness in conformer sampling: the case of small macrocycles. 55 - Hyuntae Lim, YounJoon Jung
MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning. 56 - Stefan M. Kohlbacher, Thierry Langer, Thomas Seidel
QPHAR: quantitative pharmacophore activity relationship: method and validation. 57 - Guannan Liu, Manali Singha
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. 58 - Rocco Meli
Learning protein-ligand binding affinity with atomic environment vectors. 59 - Abdul Karim
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles. 60 - Kohulan Rajan
DECIMER 1.0: deep learning for chemical image recognition using transformers. 61 - Lewis H. Mervin
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. 62 - Jason Y. C. Tam
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products. 63 - Fidele Ntie-Kang
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. 64 - Jeevan Kandel
PUResNet: prediction of protein-ligand binding sites using deep residual neural network. 65 - Stefan Mordalski
2D SIFt: a matrix of ligand-receptor interactions. 66 - Péter Árendás
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states. 67 - Feifei Guo
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network. 68 - Dingyan Wang, Jie Yu, Lifan Chen
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling. 69 - Rosa Aghdam
Using informative features in machine learning based method for COVID-19 drug repurposing. 70 - Maha A. Thafar
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning. 71 - Cédric Bouysset
ProLIF: a library to encode molecular interactions as fingerprints. 72 - Martin Sícho
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. 73 - Agnieszka Wojtuch
How can SHAP values help to shape metabolic stability of chemical compounds? 74 - Vishwesh Venkatraman
FP-ADMET: a compendium of fingerprint-based ADMET prediction models. 75 - Jules Leguy
Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization. 76 - Ulf Norinder
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning. 77 - Myriam Guillevic
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons. 78 - Jennifer Handsel
Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier. 79 - Giovanni Cincilla
Individual and collective human intelligence in drug design: evaluating the search strategy. 80 - Chao Shen, Xueping Hu
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. 81 - Alice Capecchi, Jean-Louis Reymond
Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. 82 - Kyrylo Klimenko
QSPR modeling of selectivity at infinite dilution of ionic liquids. 83 - Florian Huber
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. 84 - Xuhan Liu
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. 85 - Zi-Yi Yang, Li Fu, Ai-Ping Lu, Shao Liu, Tingjun Hou, Dong-Sheng Cao
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. 86 - Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang
Deep scaffold hopping with multimodal transformer neural networks. 87 - Francois Berenger
Molecular generation by Fast Assembly of (Deep)SMILES fragments. 88 - Jeff Guo, Jon Paul Janet, Matthias R. Bauer, Eva Nittinger
DockStream: a docking wrapper to enhance de novo molecular design. 89 - Merveille K. I. Eguida
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. 90 - Bryan Dafniet, Natacha Cerisier
Development of a chemogenomics library for phenotypic screening. 91 - Scott S. Kolmar
The effect of noise on the predictive limit of QSAR models. 92 - Jiarui Chen, Yain-Whar Si, Chon-Wai Un, Shirley W. I. Siu
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network. 93 - Daiki Erikawa, Nobuaki Yasuo
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning. 94 - Xinyu Bai, Yuxin Yin:
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development. 95 - Jaak Simm, Lina Humbeck, Adam Zalewski
Splitting chemical structure data sets for federated privacy-preserving machine learning. 96 - Zenan Zhai, Christian Druckenbrodt, Camilo Thorne
ChemTables: a dataset for semantic classification on tables in chemical patents. 97 - Zhuyifan Ye
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms. 98 - Errol L. G. Samuel
Processing binding data using an open-source workflow. 99 - David Ferro-Costas
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids. 100
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