Volume 25,
Number 1,
15 January 2004
- Sandeep Patel, Charles L. Brooks III:
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.
1-16
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- Stewart A. Adcock:
Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield.
16-27
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- Nandou Lu, David A. Kofke, Thomas B. Woolf:
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
28-40
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- Luc Claes, Jean-Pierre François, Michael S. Deleuze:
Theoretical study of the internal conversion of sulfoxide precursors of poly-isothianaphthene and related polymers.
40-50
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- Haruhiko Fukaya, Taizo Ono:
DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds.
51-60
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- Michael J. McQuaid, Huai Sun, David Rigby:
Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains.
61-71
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- Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl.
72-82
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- Manuel Piacenza, Stefan Grimme:
Systematic quantum chemical study of DNA-base tautomers.
83-99
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- Ricard Casadesús, Miquel Moreno, Àngels González-Lafont, José M. Lluch, Matthew P. Repasky:
Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry.
99-105
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- Takao Motoki, Akinobu Shiga:
New reaction simulator LUMMOX and its application for prediction of catalytic activities.
106-111
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- Martin Preuss, Wolf G. Schmidt, Kaori Seino, Jürgen Furthmüller, Friedhelm Bechstedt:
Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials.
112-122
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- Juha Linnanto, Jouko Korppi-Tommola:
Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results.
123-138
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- Ivan Tubert-Brohman, Cristiano Ruch Werneck Guimarães, Matthew P. Repasky, William L. Jorgensen:
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens.
138-150
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- Bülent Balta, Viktorya Aviyente:
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer - Erratum.
151
Electronic Edition (link) BibTeX
Volume 25,
Number 2,
30 January 2004
- Xavier Gironés, Ramon Carbó-Dorca:
TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible molecules.
153-159
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- Nohad Gresh, Gen-Bin Shi:
Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation.
160-168
Electronic Edition (link) BibTeX
- Ho-Jin Lee, Jong Hyun Kim, Hee Jung Jung, Kun-Young Kim, Eun-Jung Kim, Young-Sang Choi, Chang-Ju Yoon:
Computational study of conformational preferences of thioamide-containing azaglycine peptides.
169-178
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- Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai:
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue.
179-188
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- Célia Fonseca Guerra, Jan-Willem Handgraaf, Evert Jan Baerends, F. Matthias Bickelhaupt:
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis.
189-210
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- Thomas S. Hofer, Hung T. Tran, Christian F. Schwenk, Bernd M. Rode:
Characterization of dynamics and reactivities of solvated ions by ab initio simulations.
211-217
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- Yue Zhang, Shaowen Zhang, Qian Shu Li:
A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O CH2O + CH3.
218-226
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- Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates.
227-237
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- Holger Gohlke, David A. Case:
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
238-250
Electronic Edition (link) BibTeX
- Qian-Shu Li, Chao Yang Wang:
Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH CH2CN + H2O.
251-257
Electronic Edition (link) BibTeX
- Zheng-Wang Qu, Hui Zhu, Ze-Sheng Li, Xing-Kang Zhang, Qi-Yuan Zhang:
Density functional investigation of reaction of borohydride cation BH2+ with propylene.
258-264
Electronic Edition (link) BibTeX
- Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III:
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
265-284
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- Tamás Beke, Imre G. Csizmadia, András Perczel:
On the flexibility of -peptides.
285-307
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- Jean-Philip Piquemal, Benjamin Williams-Hubbard, Natalie Fey, Robert J. Deeth, Nohad Gresh, Claude Giessner-Prettre:
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.
308
Electronic Edition (link) BibTeX
- Yi-Gui Wang, Chérif F. Matta, Nick Henry Werstiuk:
Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation.
309-459
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Volume 25,
Number 3,
February 2004
- Vladimir Pelmenschikov, Kyung-Bin Cho, Per E. M. Siegbahn:
Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441.
311-321
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- Jennifer I. Chavez, Maira M. Carrillo, Kyle A. Beran:
Isomers of C20: An energy profile III.
322-327
Electronic Edition (link) BibTeX
- Robert J. Harrison:
Krylov subspace accelerated inexact Newton method for linear and nonlinear equations.
328-334
Electronic Edition (link) BibTeX
- Jií Kolafa:
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.
335-342
Electronic Edition (link) BibTeX
- Vinzenz Bachler:
A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function.
343-367
Electronic Edition (link) BibTeX
- A. N. Artemyev, Eduardo V. Ludeña, Valentin V. Karasiev, Antonio J. Hernández:
A finite B-spline basis set for accurate diatomic molecule calculations.
368-374
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- Luca Frediani, Roberto Cammi, Christian Silvio Pomelli, Jacopo Tomasi, Kenneth Ruud:
New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model.
375-385
Electronic Edition (link) BibTeX
- Ivan Infante, Lucas Visscher:
QM/MM study of aqueous solvation of the uranyl fluoride [UO2F42-] complex.
386-392
Electronic Edition (link) BibTeX
- Serena Donnini, André H. Juffer:
Calculation of affinities of peptides for proteins.
393-411
Electronic Edition (link) BibTeX
- Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch:
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment.
412-422
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- Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
Theoretical study on the rate constants for the C2H5 + HBr C2H6 + Br reaction.
423-428
Electronic Edition (link) BibTeX
- Rachel Crespo-Otero, Luis A. Montero, Giselle Rosquete, J. Alexander Padrón-García, Raúl H. González-Jonte:
Theoretical model of internal rotation in monosubstituted derivatives of furfural.
429-438
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- Xavier Fradera, Miquel Solà:
Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory.
439-446
Electronic Edition (link) BibTeX
- Shingo Urata, Seiji Tsuzuki, Akira Takada, Masuhiro Mikami, Tadafumi Uchimaru, Akira Sekiya:
Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3.
447-459
Electronic Edition (link) BibTeX
- Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai:
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue.
309
Electronic Edition (link) BibTeX
Volume 25,
Number 4,
March 2004
- Yi Ren, San-Yan Chu:
Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms.
461-471
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- Lingchun Song, Wei Wu, Qianer Zhang, Sason Shaik:
A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility.
472-478
Electronic Edition (link) BibTeX
- Emilio Gallicchio, Ronald M. Levy:
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
479-499
Electronic Edition (link) BibTeX
- Xiang-Yuan Li, Ke-Xiang Fu:
Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium.
500-509
Electronic Edition (link) BibTeX
- Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill:
A kinematic view of loop closure.
510-528
Electronic Edition (link) BibTeX
- Mitsunori Ikeguchi:
Partial rigid-body dynamics in NPT, NPAT and NPT ensembles for proteins and membranes.
529-541
Electronic Edition (link) BibTeX
- Michael J. Liddell, Davor Margetic, Anthony S. Mitchell, Ronald N. Warrener:
An AM1 semiempirical study of host-guest complexation in hemicarcerand complexes.
542-557
Electronic Edition (link) BibTeX
- Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br).
558-564
Electronic Edition (link) BibTeX
- S. Banu Ozkan, Hagai Meirovitch:
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin.
565-572
Electronic Edition (link) BibTeX
- Francisco Corzana, Mohammed S. Motawia, Catherine Hervé du Penhoat, Serge Pérez, Sarah M. Tschampel, Robert J. Woods, Søren Balling Engelsen:
A hydration study of (1->4) and (1->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR.
573-586
Electronic Edition (link) BibTeX
- Johannes Neugebauer, Markus Reiher:
Vibrational center-ligand couplings in transition metal complexes.
587-597
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- Shinichi Yamabe, Noriko Tsuchida:
A computational study of the role of hydrogen bonds in SN1 and E1 reactions.
598-608
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- Maxim Totrov:
Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking.
609-619
Electronic Edition (link) BibTeX
Volume 25,
Number 5,
15 April 2004
- Martin Saunders:
Stochastic search for isomers on a quantum mechanical surface.
621-626
Electronic Edition (link) BibTeX
- Richard I. Maurer, Christopher A. Reynolds:
A multilayered approach to approximating solute polarization.
627-631
Electronic Edition (link) BibTeX
- Zheng Yuan, John S. Mattick, Rohan D. Teasdale:
SVMtm: Support vector machines to predict transmembrane segments.
632-636
Electronic Edition (link) BibTeX
- John Cullen:
Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels.
637-648
Electronic Edition (link) BibTeX
- Siân T. Howard, Colin D. Abernethy:
Intramolecular CHCcarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes.
649-659
Electronic Edition (link) BibTeX
- Ali Khalaf Al-Matar, David A. Rockstraw:
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters.
660-668
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- Fan Wang, Lemin Li:
Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements.
669-677
Electronic Edition (link) BibTeX
- Michael Patra, Mikko Karttunen:
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties.
678-689
Electronic Edition (link) BibTeX
- Bülent Balta, Viktorya Aviyente:
Solvent effects on glycine II. Water-assisted tautomerization.
690-703
Electronic Edition (link) BibTeX
- Piotr Zarzycki, Robert Charmas, Pawel Szabelski:
Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach.
704-711
Electronic Edition (link) BibTeX
- Eran Eyal, Rafael Najmanovich, Brendan J. McConkey, Marvin Edelman, Vladimir Sobolev:
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.
712-724
Electronic Edition (link) BibTeX
- Paul Winget, Timothy Clark:
Enthalpies of formation from B3LYP calculations.
725-733
Electronic Edition (link) BibTeX
- D. B. Chesnut, L. D. Quin:
Nature of bonding in the sulfuryl group.
734-738
Electronic Edition (link) BibTeX
- Kazuhiro Ishida:
Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument.
739-748
Electronic Edition (link) BibTeX
- Harry A. Stern:
Simple algorithm for isothermal-isobaric molecular dynamics.
749-761
Electronic Edition (link) BibTeX
- M. Michael Gromiha, Shandar Ahmad, Makiko Suwa:
Neural network-based prediction of transmembrane -strand segments in outer membrane proteins.
762-767
Electronic Edition (link) BibTeX
- M. K. Shukla, Jerzy Leszczynski:
TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach.
768-778
Electronic Edition (link) BibTeX
Volume 25,
Number 6,
30 April 2004
- Matthias Keil, Thomas E. Exner, Jürgen Brickmann:
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network.
779-789
Electronic Edition (link) BibTeX
- David Curcó, Carlos Alemán:
Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima.
790-798
Electronic Edition (link) BibTeX
- Rochus Schmid:
Car-Parrinello simulations with a real space method.
799-812
Electronic Edition (link) BibTeX
- Jun Zeng, Daiqian Xie:
Hydrogen bonding and solvent effects on the lowest 1(n, *) excitations of triazines in water.
813-822
Electronic Edition (link) BibTeX
- Nohad Gresh, Sherif A. Kafafi, Jean-François Truchon, Dennis R. Salahub:
Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study.
823-834
Electronic Edition (link) BibTeX
- Xiang-Yuan Li, Ke-Xiang Fu, Quan Zhu, Min-Hua Shan:
Continuous medium theory for nonequilibrium solvation: II. Interaction energy between solute charge and reaction field and single-sphere model for spectral shift.
835-842
Electronic Edition (link) BibTeX
- Jinn-Moon Yang:
Development and evaluation of a generic evolutionary method for protein-ligand docking.
843-857
Electronic Edition (link) BibTeX
- Ricardo L. Mancera, Per Källblad, Nikolay P. Todorov:
Ligand-protein docking using a quantum stochastic tunneling optimization method.
858-864
Electronic Edition (link) BibTeX
- Yang Zhang, Jeffrey Skolnick:
SPICKER: A clustering approach to identify near-native protein folds.
865-871
Electronic Edition (link) BibTeX
- Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, Shiro Koseki:
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO).
872-880
Electronic Edition (link) BibTeX
- Feng Yang, Zhen-Dong Wang, Yun-Ping Huang:
Modification of the Wiener index 4.
881-887
Electronic Edition (link) BibTeX
- Fabien Pascale, C. M. Zicovich-Wilson, F. López Gejo, Bartolomeo Civalleri, Roberto Orlando, Roberto Dovesi:
The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code.
888-897
Electronic Edition (link) BibTeX
Volume 25,
Number 7,
May 2004
- Harold Basch, Mark A. Ratner:
Reduced basis set for the gold atom in cluster complexes.
899-906
Electronic Edition (link) BibTeX
- Yi Zhao, Wenguo Xu, Qian-Shu Li, Yaoming Xie, Henry F. Schaefer III:
The arsenic clusters Asn (n = 1-5) and their anions: Structures, thermochemistry, and electron affinities.
907-920
Electronic Edition (link) BibTeX
- Anatoliy Volkov, Philip Coppens:
Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning.
921-934
Electronic Edition (link) BibTeX
- Alexander H. Boschitsch, Marcia O. Fenley:
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation.
935-955
Electronic Edition (link) BibTeX
- Juan Cortés, Thierry Siméon, Magali Remaud-Siméon, Vinh Tran:
Geometric algorithms for the conformational analysis of long protein loops.
956-967
Electronic Edition (link) BibTeX
- Xiaoping Han, Yue Zhang, Huibin Xu:
First-principles pair potentials across the metal-ceramic interface.
968-973
Electronic Edition (link) BibTeX
- Massimiliano Aschi, Costantino Zazza, Riccardo Spezia, Cecilia Bossa, Alfredo Di Nola, Maurizio Paci, Andrea Amadei:
Conformational fluctuations and electronic properties in myoglobin.
974-984
Electronic Edition (link) BibTeX
- Arnaud Blondel:
Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions.
985-993
Electronic Edition (link) BibTeX
- Mihai V. Putz, Nino Russo, Emilia Sicilia:
On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluation.
994-1003
Electronic Edition (link) BibTeX
Volume 25,
Number 8,
June 2004
- Olgun Guvench, Charles L. Brooks III:
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
1005-1014
Electronic Edition (link) BibTeX
- Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong:
A semi-implicit solvent model for the simulation of peptides and proteins.
1015-1029
Electronic Edition (link) BibTeX
- Delano P. Chong, Erik Van Lenthe, Stan J. A. van Gisbergen, Evert Jan Baerends:
Even-tempered slater-type orbitals revisited: From hydrogen to krypton.
1030-1036
Electronic Edition (link) BibTeX
- Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar:
A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints.
1037-1046
Electronic Edition (link) BibTeX
- Anil Kumar, Michaela Knapp-Mohammady, P. C. Mishra, Sándor Suhai:
A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs.
1047-1059
Electronic Edition (link) BibTeX
- Arturo Robertazzi, James A. Platts:
Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study.
1060-1067
Electronic Edition (link) BibTeX
- Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Ortoleva:
Efficient solution technique for solving the Poisson-Boltzmann equation.
1068-1074
Electronic Edition (link) BibTeX
- Leslaw K. Bieniasz:
Improving the accuracy of the spatial discretization in finite-difference electrochemical kinetic simulations, by means of the extended Numerov method.
1075-1083
Electronic Edition (link) BibTeX
- András Perczel, Péter Hudáky, Anna K. Füzéry, Imre G. Csizmadia:
Stability issues of covalently and noncovalently bonded peptide subunits.
1084-1100
Electronic Edition (link) BibTeX
- Zlatko Vasilkoski, David L. Weaver:
Diffusion-collision model algorithms for protein folding kinetics.
1101-1107
Electronic Edition (link) BibTeX
Volume 25,
Number 9,
15 July 2004
- Publisher's note: Sir John A. Pople, 1925-2004.
1108
Electronic Edition (link) BibTeX
- J. Ulises Reveles, Andreas M. Köster:
Geometry optimization in density functional methods.
1109-1116
Electronic Edition (link) BibTeX
- Andy Becue, Nathalie Meurice:
Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density.
1117-1126
Electronic Edition (link) BibTeX
- Kenneth B. Wiberg, Yi-Gui Wang:
Conformational energies for 2-substituted butanes.
1127-1132
Electronic Edition (link) BibTeX
- Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe:
Sampling protein conformations and pathways.
1133-1148
Electronic Edition (link) BibTeX
- Genyuan Li, Jacqueline Schoendorf, Tak-San Ho, Herschel Rabitz:
Multicut-HDMR with an application to an ionospheric model.
1149-1156
Electronic Edition (link) BibTeX
- Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case:
Development and testing of a general amber force field.
1157-1174
Electronic Edition (link) BibTeX
- Hiroaki Umeda, Shiro Koseki, Umpei Nagashima:
Improvement of parallelization performance of GAMESS: Global sum and (semi-)direct integral calculation in multireference perturbation calculation.
1175-1183
Electronic Edition (link) BibTeX
- Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study on the mechanism of the 1CHCl + NO2 reactions.
1184-1190
Electronic Edition (link) BibTeX
- Sergio Aragon:
A precise boundary element method for macromolecular transport properties.
1191-1205
Electronic Edition (link) BibTeX
- Christopher C. Lovallo, Mariusz Klobukowski:
Improved model core potentials for the second- and third-row transition metals.
1206-1213
Electronic Edition (link) BibTeX
Volume 25,
Number 10,
30 July 2004
- Delia Soto-Castro, Patricia Guadarrama:
Macrocyclic vs. dendrimeric effect. A DFT study.
1215-1226
Electronic Edition (link) BibTeX
- Ignacio Fdez. Galván, M. E. Martín, M. A. Aguilar:
A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation.
1227-1233
Electronic Edition (link) BibTeX
- David Muñoz, Coen de Graaf, Francesc Illas:
Putting error bars on the Ab Initio theoretical estimates of the magnetic coupling constants: The parent compounds of superconducting cuprates as a case study.
1234-1241
Electronic Edition (link) BibTeX
- Martin Almlöf, Bjørn O. Brandsdal, Johan Åqvist:
Binding affinity prediction with different force fields: Examination of the linear interaction energy method.
1242-1254
Electronic Edition (link) BibTeX
- Nisanth N. Nair, Thomas Bredow, Karl Jug:
Molecular dynamics implementation in MSINDO: Study of silicon clusters.
1255-1263
Electronic Edition (link) BibTeX
- K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena:
ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure.
1264-1276
Electronic Edition (link) BibTeX
- Wolfgang Quapp:
Reaction pathways and projection operators: Application to string methods.
1277-1285
Electronic Edition (link) BibTeX
- Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine.
1286-1294
Electronic Edition (link) BibTeX
- Robert M. Dirks, Niles A. Pierce:
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.
1295-1304
Electronic Edition (link) BibTeX
- Gordon M. Crippen:
Cluster distance geometry of polypeptide chains.
1305-1312
Electronic Edition (link) BibTeX
Volume 25,
Number 11,
August 2004
- Yuri A. Kosinsky, Pavel E. Volynsky, Philippe Lagant, Gérard Vergoten, Ei-Ichiro Suzuki, Alexander S. Arseniev, Roman G. Efremov:
Development of the force field parameters for phosphoimidazole and phosphohistidine.
1313-1321
Electronic Edition (link) BibTeX
- Marina Udier-Blagovi, Patricia Morales De Tirado, Shoshannah A. Pearlman, William L. Jorgensen:
Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
1322-1332
Electronic Edition (link) BibTeX
- Roberto Improta, Vincenzo Barone:
Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions.
1333-1341
Electronic Edition (link) BibTeX
- Kenneth B. Wiberg:
Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ.
1342-1346
Electronic Edition (link) BibTeX
- Jaime Fernández Rico, R. López, I. Ema, G. Ramírez:
Electrostatic potentials and fields from density expansions of deformed atoms in molecules.
1347-1354
Electronic Edition (link) BibTeX
- Jaime Fernández Rico, R. López, G. Ramírez, I. Ema, E. V. Ludeña:
Analytical method for the representation of atoms-in-molecules densities.
1355-1363
Electronic Edition (link) BibTeX
- Bo Liao, Tian-Ming Wang:
New 2D graphical representation of DNA sequences.
1364-1368
Electronic Edition (link) BibTeX
- Gennady N. Chuev, Maxim V. Fedorov:
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model.
1369-1377
Electronic Edition (link) BibTeX
- Aisha El-Sherbiny, Raymond A. Poirier:
An evaluation of the radial part of numerical integration commonly used in DFT.
1378-1384
Electronic Edition (link) BibTeX
- Dawoon Jung, Jie Floyd, Tamara M. Gund:
A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands.
1385-1399
Electronic Edition (link) BibTeX
- Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III:
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
1400-1415
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- Peter A. Sims, Chung F. Wong, James Andrew McCammon:
Charge optimization of the interface between protein kinases and their ligands.
1416-1429
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Volume 25,
Number 12,
September 2004
- Yun Xiang, Da W. Zhang, John Z. H. Zhang:
Fully quantum mechanical energy optimization for protein-ligand structure.
1431-1437
Electronic Edition (link) BibTeX
- Jörg-Rüdiger Hill, Johann Plank:
Retardation of setting of plaster of Paris by organic acids: Understanding the mechanism through molecular modeling.
1438-1448
Electronic Edition (link) BibTeX
- Hui Li, Jan H. Jensen:
Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation.
1449-1462
Electronic Edition (link) BibTeX
- Stefan Grimme:
Accurate description of van der Waals complexes by density functional theory including empirical corrections.
1463-1473
Electronic Edition (link) BibTeX
- Tim N. Heinz, Philippe H. Hünenberger:
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions.
1474-1486
Electronic Edition (link) BibTeX
- Daiqian Xie, Jun Zeng:
Hydrogen bonding and solvatochromatic shift of the lowest 1(n, *) excitation of s-tetrazine in its hydrated clusters and dilute solutions.
1487-1495
Electronic Edition (link) BibTeX
- Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Fariba Taghavi:
Application of ab initio theory to QSAR study of 1, 4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures.
1495-1503
Electronic Edition (link) BibTeX
- Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III:
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
1504-1514
Electronic Edition (link) BibTeX
- Leslaw K. Bieniasz:
A fourth-order accurate, Numerov-type, three-point finite-difference discretization of electrochemical reaction-diffusion equations on nonuniform (exponentially expanding) spatial grids in one-dimensional space geometry.
1515-1521
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- Ilona Hudáky, Péter Hudáky, András Perczel:
Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model.
1522-1531
Electronic Edition (link) BibTeX
- Christian Silvio Pomelli:
A tessellationless integration grid for the polarizable continuum model reaction field.
1532-1541
Electronic Edition (link) BibTeX
- Xavier López, Jorge A. Fernández, Susanna Romo, Jean François Paul, Leonid Kazansky, Josep M. Poblet:
Are the solvent effects critical in the modeling of polyoxoanions?
1542-1549
Electronic Edition (link) BibTeX
Volume 25,
Number 13,
October 2004
- Karl Jug, Thomas Bredow:
Models for the treatment of crystalline solids and surfaces.
1551-1567
Electronic Edition (link) BibTeX
- Holger Merlitz, Thomas Herges, Wolfgang Wenzel:
Fluctuation analysis and accuracy of a large-scale in silico screen.
1568-1575
Electronic Edition (link) BibTeX
- Chinapong Kritayakornupong, Kristof Plankensteiner, Bernd M. Rode:
Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.
1576-1583
Electronic Edition (link) BibTeX
- Alexander D. MacKerell Jr.:
Empirical force fields for biological macromolecules: Overview and issues.
1584-1604
Electronic Edition (link) BibTeX
- Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin:
UCSF Chimera - A visualization system for exploratory research and analysis.
1605-1612
Electronic Edition (link) BibTeX
- Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten:
Classical force field parameters for the heme prosthetic group of cytochrome c.
1613-1622
Electronic Edition (link) BibTeX
- Jason Wagoner, Nathan A. Baker:
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models.
1623-1629
Electronic Edition (link) BibTeX
- Richard E. Gillilan, Ryan H. Lilien:
Optimization and dynamics of protein-protein complexes using B-splines.
1630-1646
Electronic Edition (link) BibTeX
- Maria Del Carmen Michelini, Nino Russo, Mohammad Esmaïl Alikhani, Bernard Silvi:
Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules.
1647-1655
Electronic Edition (link) BibTeX
- Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren:
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.
1656-1676
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:07:17 2009
by Michael Ley (ley@uni-trier.de)