default search action
Journal of Computational Chemistry, Volume 26
Volume 26, Number 1, January 2005
- Kaori Fukuzawa
, Kazuo Kitaura, Masami Uebayasi, Kotoko Nakata, Tsuguchika Kaminuma, Tatsuya Nakano:
Ab initio quantum mechanical study of the binding energies of human estrogen receptor with its ligands: An application of fragment molecular orbital method. 1-10 - Maria Kontoyianni, Glenn S. Sokol, Laura M. McCellan:
Evaluation of library ranking efficacy in virtual screening. 11-22 - Steven L. Dixon, Kenneth M. Merz Jr.
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. 23-34 - Zhong-Zhi Yang, Li-Dong Gong, Dong-Xia Zhao, Ming-Bo Zhang:
Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules. 35-47 - Art E. Cho, John A. Wendel, Nagarajan Vaidehi, Peter M. Kekenes-Huskey, Wely B. Floriano
The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals. 48-71 - Malek O. Khan, Gareth Kennedy, Derek Y. C. Chan:
A scalable parallel Monte Carlo method for free energy simulations of molecular systems. 72-77 - Kyoungrim Lee, Cezary Czaplewski
An efficient molecular docking using conformational space annealing. 78-87 - Bing Suo, Gaohong Zhai, Yubin Wang, Zhenyi Wen, Xiangqian Hu, Lemin Li:
Parallelization of MRCI based on hole-particle symmetry. 88-96 - F. Martin, Hendrik Zipse:
Charge distribution in the water molecule - A comparison of methods. 97-105 - Wenli Zou, Wenjian Liu
Extensive theoretical studies on the low-lying electronic states of indium monochloride cation, InCl+. 106-113
- Junmei Wang
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field" Journal of Computational Chemistry(2004) 25(9) 1157-1174. 114-
Volume 26, Number 2, January 2005
- Serena Donnini, Alan E. Mark, André H. Juffer
Incorporating the effect of ionic strength in free energy calculations using explicit ions. 115-122 - Robert J. Deeth
DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment. 123-130 - David de Sancho
Evolutionary method for the assembly of rigid protein fragments. 131-141 - Daniela Bertolini Depizzol
MoCalc: A new graphical user interface for molecular calculations. 142-144 - Zuzana Benková
Reduced-size polarized basis sets for calculations of molecular electric properties. I. The basis set generation. 145-153 - Roma E. Oakes, Steven E. J. Bell, Zuzana Benková
Reduced-size polarized basis sets for calculations of molecular electric properties. II. Simulation of the Raman spectra. 154-159 - Mitsuhito Wada, Minoru Sakurai:
A quantum chemical method for rapid optimization of protein structures. 160-168 - H. Sun, Paul W.-C. Kung:
Urea: An ab initio and force field study of the gas and solid phases. 169-174 - Sandro Chiodo, Nino Russo
Newly developed basis sets for density functional calculations. 175-184 - Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study and rate constant calculation for the reactions of SH (SD) with Cl2, Br2, and BrCl. 184-193 - W. Dean Harman, Carl Trindle:
Charge donation to and dearomatization of benzene attending complexation: DFT estimates of binding energies of TpMXO(L) with benzene, for Tp = hydridotris(pyrazolyl) borate, MXO = MoNO, ReCO, and WNO, and L = ammonia, N-methylimidazole, pyridine, phosphine, methyl isocyanide, and carbon monoxide. 194-200
Volume 26, Number 3, February 2005
- K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena:
Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology. 201-213 - Robert J. Gdanitz, Gary D. Black, Carina Lansing, Bruce J. Palmer
Registering the Amica electronic structure code in the Extensible Computational Chemistry Environment. 214-225 - Yuhui Qu, Xiufang Bian:
Electronic structure and stability of AlnPn (n = 2-4) clusters. 226-234 - Joanna Makowska, Mariusz Makowski
Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force. 235-242 - Charles F. F. Karney
Method for computing protein binding affinity. 243-251 - Matthew A. Meineke, Charles F. Vardeman II
OOPSE: An object-oriented parallel simulation engine for molecular dynamics. 252-271 - Minoru Saito, Isao Okazaki, Masayuki Oda
A free energy calculation study of the effect of HF substitution on binding affinity in ligand-antibody interactions. 272-282 - F. Wennmohs, M. Schindler:
Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high-level ab initio interaction energies. 283-293 - Josef Seda, Jaroslav V. Burda, Jerzy Leszczynski:
Study of electronic spectra of free-base porphin and Mg-porphin: Comprehensive comparison of variety of ab initio, DFT, and semiempirical methods. 294-303 - Panagiotis G. Karamertzanis
Ab initio crystal structure prediction - I. Rigid molecules. 304-324
Volume 26, Number 4, March 2005
- Yasuyo Hatano, Shigeyoshi Yamamoto, Hiroshi Tatewaki:
Characterization of molecular orbitals by counting nodal regions. 325-333 - Shura Hayryan, Chin-Kun Hu
A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients. 334-343 - Ángel Martín Pendás
Two-electron integrations in the Quantum Theory of Atoms in Molecules with correlated wave functions. 344-351 - Michael Meyer, Alexandre Hocquet
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. 352-364 - Pablo Campomanes
Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: A computational study. 365-373 - Eckart Bindewald, Jeffrey Skolnick:
A scoring function for docking ligands to low-resolution protein structures. 374-383 - Philippe Carbonniere, Tecla Lucca, Claude Pouchan, Nadia Rega
Vibrational computations beyond the harmonic approximation: Performances of the B3LYP density functional for semirigid molecules. 384-388 - Mehdi Mobli
Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis. 389-398 - Quan Zhu, Ke-Xiang Fu, Xiang-Yuan Li, Zhen Gong, Jian-Yi Ma:
Continuous medium theory for nonequilibrium solvation: III. Solvation shift by monopole approximation and multipole expansion in spherical cavity. 399-409
Volume 26, Number 5, April 2005
- Veronika Kasalová, Henry F. Schaefer III:
Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn-(n = 1-8). 411-435 - Mari Tamaoki, Yusuke Yamauchi, Hiromi Nakai
Short-time Fourier transform analysis of ab initio molecular dynamics simulation: Collision reaction between CN and C4H6. 436-442 - Rajeev Prabhakar, Keiji Morokuma, Djamaladdin G. Musaev:
A comparative study of various computational approaches in calculating the structure of pyridoxal 5r-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment. 443-446 - Robert Ponec, Gleb Yuzhakov, Markku R. Sundberg:
Chemical structures from the analysis of domain-averaged fermi holes. Nature of the Mn-Mn bond in bis(pentacarbonylmanganese). 447-454 - Ana Gallegos
Maximal probability domains in linear molecules. 455-460 - Qishi Du, Paul G. Mezey, Kuo-Chen Chou:
Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives. 461-470 - Carlos A. Stortz:
Comparative performance of MM3(92) and two TINKERTM MM3 versions for the modeling of carbohydrates. 471-483 - Bing Liu, Jiaju Zhou:
SARS-CoV protease inhibitors design using virtual screening method from natural products libraries. 484-490 - Andrei M. Tokmachev
Transferability of parameters of strictly local geminals' wave function and possibility of sequential derivation of molecular mechanics. 491-505 - Pierre Tufféry
Improved greedy algorithm for protein structure reconstruction. 506-513
- Lingchun Song, Yirong Mo, Qianer Zhang, Wei Wu:
XMVB: A program for ab initio nonorthogonal valence bond computations. 514-521
Volume 26, Number 6, April 2005
- Raúl A. Bustos Marún, Eduardo A. Coronado
Fitting complex potential energy surfaces to simple model potentials: Application of the simplex-annealing method. 523-531 - Vinzenz Bachler:
The behavior of transition metal nitrido bonds towards protonation rationalized by means of localized bonding schemes and their weights. 532-551 - Ping Li, Yuxiang Bu:
Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase. 552-560 - Peter L. Cummins, Jill E. Gready:
Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. 561-568 - Núria González-García, Àngels González-Lafont
Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH. 569-583 - Qingyu Kong, Li Zhao, Wenning Wang, Chen Wang, Can Xu
Magic number silicon dioxide-based clusters: Laser ablation-mass spectrometric and density functional theory studies. 584-598 - Peter Pulay, Svein Saebo, Massimo Malagoli, Jon Baker:
Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules. 599-605 - T. K. Manojkumar, Chunzhi Cui, Kwang S. Kim
Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine. 606-611 - Pedro L. Muiño:
The OH. + CH3SH reaction: Support for an addition-elimination mechanism from ab initio calculations. 612-618 - Manfred Rudolph:
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. I. Presentation of the basic concept and application to a pure diffusion system. 619-632 - Manfred Rudolph:
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. II. Application to systems comprising first-order chemical reactions. 633-641 - Hong-Qing He, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study for the reaction of CH3OCl with Cl atom. 642-650
Volume 26, Number 7, May 2005
- Eva Darian, Vladimir Hnizdo, Adam Fedorowicz, Harshinder Singh, Eugene Demchuk:
Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations. 651-660 - Marcus Lundberg, Per E. M. Siegbahn:
Agreement between experiment and hybrid DFT calculations for OH bond dissociation enthalpies in manganese complexes. 661-667 - Peter A. Sims
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. 668-681 - Eric J. Sorin, Vijay S. Pande:
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. 682-690 - Min-Yi Shen, Karl F. Freed:
A simple method for faster nonbonded force evaluations. 691-698 - L. Renee Olano, Steven W. Rick:
Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials. 699-707 - Alán Aspuru-Guzik
A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo. 708-715 - Anti Liivat, Alvo Aabloo
Development of a force field for Li2SiF6. 716-724 - Thereza A. Soares
An improved nucleic acid parameter set for the GROMOS force field. 725-737 - Fredrik Blomgren, Sven Larsson:
Exploring the potential energy surface of retinal, a comparison of the performance of different methods. 738-742 - Neil Gohaud, Didier Bégué
New parallel software (P_Anhar) for anharmonic vibrational calculations: Application to (CH3Li)2. 743-754
Volume 26, Number 8, June 2005
- Robert J. Petrella, Martin Karplus:
Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. 755-787 - Hirofumi Fujimoto, Miroslav Pinak, Toshiyuki Nemoto, Peter O'Neill, Etsuo Kume, Kimiaki Saito, Hideaki Maekawa:
Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site. 788-798 - Si-Dian Li, Chang-Qing Miao, Jin-Chang Guo, Guang-Ming Ren:
Carbon boronyls: Species with higher viable possibility than boron carbonyls at the density functional theory. 799-802 - Frank J. Owens:
Stability of (C60)2 and epoxide dimers, (C60)2ON, and their anions. 803-806 - Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study on the reaction mechanism of the methyl radical with nitrogen oxides. 807-817 - Akifumi Oda, Noriyuki Yamaotsu
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models. 818-826 - Alessandro Genoni
Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. 827-835 - Theodore S. Dibble
Computations on the A-X transition of isoprene-OH-O2 peroxy radicals. 836-845 - Jaime Fernández Rico, Ramón López, Ignacio Ema, Guillermo Ramírez
Translation of STO charge distributions. 846-855
- Alán Aspuru-Guzik
Zori 1.0: A parallel quantum Monte Carlo electronic structure package. 856-862
- Jason Wagoner, Nathan A. Baker:
Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, " by Jason Wagoner and Nathan A. Baker. 863-
Volume 26, Number 9, July 2005
- Ia. I. Dobrogorskaia-Méreau, Alexander V. Nemukhin
Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion. 865-870 - Gui-Chang Wang
The relationship between adsorption energies of methyl on metals and the metallic electronic properties: A first-principles DFT study. 871-878 - Andreas Schreiber, Michael Humbert, Alexander Benz, Ursula Dietrich
3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins. 879-887 - Per E. M. Siegbahn, Alexander F. Shestakov:
Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase. 888-898 - Wayne J. Pullan:
An unbiased population-based search for the geometry optimization of Lennard-Jones clusters: 2 leq N leq 372. 899-906 - Jaroslav V. Burda, Michal Zeizinger, Jerzy Leszczynski:
Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters. 907-914 - Art E. Cho, Victor Guallar
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach. 915-931 - Roberto L. A. Haiduke
An accurate relativistic universal Gaussian basis set for hydrogen through Nobelium without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models. 932-940 - Illia Horenko, Sönke Lorenz, Christof Schütte, Wilhelm Huisinga
Adaptive approach for nonlinear sensitivity analysis of reaction kinetics. 941-948 - Thomas S. Hofer
Structure-breaking effects of solvated Rb(I) in dilute aqueous solution - An ab initio QM/MM MD approach. 949-956 - Sanjay Banerjee
Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics. 957-967
Volume 26, Number 10, July 2005
- Li Yang, Ji-Kang Feng, Ai-Min Ren:
Theoretical studies on the electronic and optical properties of two new alternating fluorene/carbazole copolymers. 969-979 - Chang-Guo Zhan, Shi-Xian Deng, Jaime G. Skiba, Beth A. Hayes, Sarah M. Tschampel, George C. Shields
First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine. 980-986 - Toru Inaba, Saisei Tahara
All-electron density functional calculation on insulin with quasi-canonical localized orbitals. 987-993 - Ying Xue
DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. 994-1005 - G. Theodoor De Jong, Daan P. Geerke
Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study. 1006-1020 - Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre:
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms. 1021-1031 - Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang:
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. 1032-1041 - Stefano Borini, Daniel Maynau, Stefano Evangelisti:
A combined freeze-and-cut strategy for the description of large molecular systems using a localized orbitals approach. 1042-1051 - Jean-Philip Piquemal
A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution. 1052-1062 - Jerod Parsons
Practical conversion from torsion space to Cartesian space for in silico protein synthesis. 1063-1068 - Lesley D. Lloyd, Roy L. Johnston
Strategies for increasing the efficiency of a genetic algorithm for the structural optimization of nanoalloy clusters. 1069-1078 - Piotr Zarzycki
Role of the surface heterogeneity in adsorption of hydrogen ions on metal oxides: Theory and simulations. 1079-1088
Volume 26, Number 11, August 2005
- Anatoly M. Ruvinsky, A. V. Kozintsev:
New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. 1089-1095 - Caterina Benzi, Maurizio Cossi
Building cavities in a fluid of spherical or rod-like particles: A contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model. 1096-1105 - Michael S. Schuurman
The ab initio limit quartic force field of BH3. 1106-1112 - Nohad Gresh, Jean-Philip Piquemal
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. 1113-1130 - Jens Antony, Jean-Philip Piquemal
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. 1131-1147 - Siegfried Höfinger:
Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2. 1148-1154 - András Perczel, Zoltán Gáspári, Imre G. Csizmadia:
Structure and stability of -pleated sheets. 1155-1168 - Florian Koskowski, Bernd Hartke
Towards protein folding with evolutionary techniques. 1169-1179 - Maxence Launay, Richard Dronskowski
A theoretical study on the structures and energetics of hypothetical TiM(NCN)3 compounds of the 3d transition metals. 1180-1188 - Hongzhi Li, Yaoqi Zhou
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation. 1189-1192 - Manfred Rudolph:
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. Part 3. Application to electrochemical systems comprising second-order chemical reactions. 1193-1204
Volume 26, Number 12, September 2005
- Robert Ponec, Joaquin Chaves:
Electron pairing and chemical bonds. Electron fluctuation and pair localization in ELF domains. 1205-1213 - Zexing Cao, Qianer Zhang:
Computational analyses of singlet-singlet and singlet-triplet transitions in mononuclear gold-capped carbon-rich conjugated complexes. 1214-1221 - Po-Ssu Huang
Adaptation of a fast Fourier transform-based docking algorithm for protein design. 1222-1232 - Thanh Ha Nguyen
Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: Implications for the design of synthetic dicarboxylic acid receptors. 1233-1241 - Andreas W. Götz
Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT. 1242-1253 - J. M. Junquera-Hernández
Multistate active spaces from local CAS-SCF molecular orbitals: The photodissociation of HFCO as an example. 1254-1262 - Xue-Hai Ju, Xin Wang, Feng-Li Bei:
Substituent effects on heats of formation, group interactions, and detonation properties of polyazidocubanes. 1263-1269 - Marek Freindorf, Yihan Shao
Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential. 1270-1278 - Zhigang Wang
A path from Ih to C1 symmetry for C20 cage molecule. 1279-1283 - Maria Del Carmen Michelini, Nino Russo
Energetic and topological analyses of the oxidation reaction between Mon (n = 1, 2) and N2O. 1284-1293 - Christian Bartels
Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations. 1294-1305
Volume 26, Number 13, October 2005
- Péter Hudáky, András Perczel:
Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI. Chemical shift analysis of his to gain 3D structure and protonation state information. 1307-1317 - David E. Shaw:
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. 1318-1328 - Pathumwadee Intharathep, Anan Tongraar, Kritsana Sagarik:
Structure and dynamics of hydrated NH4+: An ab initio QM/MM molecular dynamics simulation. 1329-1338 - Yu-Hua Yao, Xu-Ying Nan, Tian-Ming Wang:
A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them. 1339-1346 - Raquel Villar, María J. Gil, J. I. García, Victor Martínez-Merino
Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? 1347-1358 - Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins. 1359-1371 - Hitoshi Kusama
Theoretical study of quinolines-I2 intermolecular interaction and implications on dye-sensitized solar cell performance. 1372-1382 - Zoe Cournia
A molecular mechanics force field for biologically important sterols. 1383-1399 - Roberto D. Lins
A new GROMOS force field for hexopyranose-based carbohydrates. 1400-1412 - Youdong Lin, Mark A. Stadtherr:
Deterministic global optimization of molecular structures using interval analysis. 1413-1420 - Hui Zhang, Jia-Yan Wu, Ze-Sheng Li, Jing-Yao Liu, Li Sheng, Chia-Chung Sun:
Dual-level direct dynamics studies on the reaction Cl + CHBr2Cl. 1421-1426
Volume 26, Number 14, November 2005
- Victor Polo, Juan Andrés
A joint study based on the electron localization function and catastrophe theory of the chameleonic and centauric models for the Cope rearrangement of 1, 5-hexadiene and its cyano derivatives. 1427-1437 - Gernot Katzer, Alexander F. Sax:
Identification and thermodynamic treatment of several types of large-amplitude motions. 1438-1451 - Alba T. Macias
CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field. 1452-1463 - Nicholas P. Labello, Antonio M. Ferreira
An augmented effective core potential basis set for the calculation of molecular polarizabilities. 1464-1471 - Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. 1472-1486 - Daiqian Xie, Jun Zeng
Electronic excitations of green fluorescent proteins: Protonation states of chromophore model compound in solutions. 1487-1496 - A. Patrícia Bento, Miquel Solà
Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si). 1497-1504 - Max C. Holthausen
Benchmarking approximate density functional theory. I. s/d excitation energies in 3d transition metal cations. 1505-1518 - Bo Liao, Kequan Ding:
Graphical approach to analyzing DNA sequences. 1519-1523 - Ricardo Oliveira Freire, Gerd Bruno Rocha
Modeling lanthanide complexes: Sparkle/AM1 parameters for ytterbium (III). 1524-1528 - Daniel J. Price, Charles L. Brooks III:
Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA. 1529-1541
Volume 26, Number 15, November 2005
- Hui-Yin Wu, Ajay Chaudhari
Theoretical studies on nonlinear optical properties of formaldehyde oligomers by ab initio and density functional theory methods. 1543-1564 - Jianhan Chen, Wonpil Im, Charles L. Brooks III:
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. 1565-1578 - Maxim Tafipolsky, Rochus Schmid
Calculation of rotational partition functions by an efficient Monte Carlo importance sampling technique. 1579-1591 - Chompoonut Rungnim
A density functional study of propylene glycol conversion to propanal and propanone of various acid-catalyzed reaction models: A water-addition effect. 1592-1599 - Yoong-Kee Choe
Effect of the axial cysteine ligand on the electronic structure and reactivity of high-valent iron(IV) oxo-porphyrins (Compound I): A theoretical study. 1600-1611 - Sanghyun Park, Randall J. Radmer, Teri E. Klein
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides. 1612-1616 - Shantenu Jha
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer. 1617-1627 - Emanuel H. Rubensson, Pawel Salek:
Systematic sparse matrix error control for linear scaling electronic structure calculations. 1628-1637 - Mark T. Oakley
Lattice models of peptide aggregation: Evaluation of conformational search algorithms. 1638-1646 - Michael A. Johnston
Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. 1647-1659 - Gerald R. Kneller
Comment on Using quaternions to calculate RMSD [J. Comp. Chem. 25, 1849 (2004)]. 1660-1662 - Evangelos A. Coutsias
Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. 1663-1665
Volume 26, Number 16, December 2005
- Charles L. Brooks III:
Editorial. 1667 - David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo
The Amber biomolecular simulation programs. 1668-1688 - William L. Jorgensen, Julian Tirado-Rives
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. 1689-1700 - David van der Spoel
GROMACS: Fast, flexible, and free. 1701-1718 - Markus Christen, Philippe H. Hünenberger
The GROMOS software for biomolecular simulation: GROMOS05. 1719-1751 - Jay L. Banks, Hege S. Beard, Yixiang X. Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert B. Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Yu Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy:
Integrated Modeling Program, Applied Chemical Theory (IMPACT). 1752-1780 - James C. Phillips
Scalable molecular dynamics with NAMD. 1781-1802
- David E. Shaw:
Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. 1803
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-12-29 01:16 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by: