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
Electronic Edition (link) BibTeX
- Maria Kontoyianni, Glenn S. Sokol, Laura M. McCellan:
Evaluation of library ranking efficacy in virtual screening.
11-22
Electronic Edition (link) BibTeX
- Steven L. Dixon, Kenneth M. Merz Jr., Giorgio Lauri, James C. Ianni:
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method.
23-34
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Art E. Cho, John A. Wendel, Nagarajan Vaidehi, Peter M. Kekenes-Huskey, Welly B. Floriano, Prabal K. Maiti, William A. Goddard III:
The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals.
48-71
Electronic Edition (link) BibTeX
- Malek O. Khan, Gareth Kennedy, Derek Y. C. Chan:
A scalable parallel Monte Carlo method for free energy simulations of molecular systems.
72-77
Electronic Edition (link) BibTeX
- Kyoungrim Lee, Cezary Czaplewski, Seung-Yeon Kim, Jooyoung Lee:
An efficient molecular docking using conformational space annealing.
78-87
Electronic Edition (link) BibTeX
- Bing Suo, Gaohong Zhai, Yubin Wang, Zhenyi Wen, Xiangqian Hu, Lemin Li:
Parallelization of MRCI based on hole-particle symmetry.
88-96
Electronic Edition (link) BibTeX
- F. Martin, H. Zipse:
Charge distribution in the water molecule - A comparison of methods.
97-105
Electronic Edition (link) BibTeX
- Wenli Zou, Wenjian Liu:
Extensive theoretical studies on the low-lying electronic states of indium monochloride cation, InCl+.
106-113
Electronic Edition (link) BibTeX
Erratum
Volume 26,
Number 2,
January 2005
- Serena Donnini, Alan E. Mark, André H. Juffer, Alessandra Villa:
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
115-122
Electronic Edition (link) BibTeX
- Robert J. Deeth, Natalie Fey, Benjamin Williams-Hubbard:
DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment.
123-130
Electronic Edition (link) BibTeX
- David de Sancho, Lidia Prieto, Ana M. Rubio, Antonio Rey:
Evolutionary method for the assembly of rigid protein fragments.
131-141
Electronic Edition (link) BibTeX
- Daniela Bertolini Depizzol, Marcia Helena Moreira Paiva, Thiago Oliveira Dos Santos, Anderson Coser Gaudio:
MoCalc: A new graphical user interface for molecular calculations.
142-144
Electronic Edition (link) BibTeX
- Zuzana Benkova, Andrzej J. Sadlej, Roma E. Oakes, Steven E. J. Bell:
Reduced-size polarized basis sets for calculations of molecular electric properties. I. The basis set generation.
145-153
Electronic Edition (link) BibTeX
- Roma E. Oakes, Steven E. J. Bell, Zuzana Benkova, Andrzej J. Sadlej:
Reduced-size polarized basis sets for calculations of molecular electric properties. II. Simulation of the Raman spectra.
154-159
Electronic Edition (link) BibTeX
- Mitsuhito Wada, Minoru Sakurai:
A quantum chemical method for rapid optimization of protein structures.
160-168
Electronic Edition (link) BibTeX
- H. Sun, Paul W.-C. Kung:
Urea: An ab initio and force field study of the gas and solid phases.
169-174
Electronic Edition (link) BibTeX
- Sandro Chiodo, Nino Russo, Emilia Sicilia:
Newly developed basis sets for density functional calculations.
175-184
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Robert J. Gdanitz, Gary D. Black, Carina Lansing, Bruce J. Palmer, Karen Schuchardt:
Registering the Amica electronic structure code in the Extensible Computational Chemistry Environment.
214-225
Electronic Edition (link) BibTeX
- Yuhui Qu, Xiufang Bian:
Electronic structure and stability of AlnPn (n = 2-4) clusters.
226-234
Electronic Edition (link) BibTeX
- Joanna Makowska, Mariusz Makowski, Adam Liwo, Lech Chmurzynski:
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
Electronic Edition (link) BibTeX
- Charles F. F. Karney, Jason E. Ferrara, Stephan Brunner:
Method for computing protein binding affinity.
243-251
Electronic Edition (link) BibTeX
- Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J. Fennell, J. Daniel Gezelter:
OOPSE: An object-oriented parallel simulation engine for molecular dynamics.
252-271
Electronic Edition (link) BibTeX
- Minoru Saito, Isao Okazaki, Masayuki Oda, Ikuo Fujii:
A free energy calculation study of the effect of HF substitution on binding affinity in ligand-antibody interactions.
272-282
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Panagiotis G. Karamertzanis, Constantinos C. Pantelides:
Ab initio crystal structure prediction - I. Rigid molecules.
304-324
Electronic Edition (link) BibTeX
Volume 26,
Number 4,
March 2005
- Yasuyo Hatano, Shigeyoshi Yamamoto, Hiroshi Tatewaki:
Characterization of molecular orbitals by counting nodal regions.
325-333
Electronic Edition (link) BibTeX
- Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Edik Hayryan, Imrich Pokorný:
A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients.
334-343
Electronic Edition (link) BibTeX
- A. Martín Pendás, E. Francisco, M. A. Blanco:
Two-electron integrations in the Quantum Theory of Atoms in Molecules with correlated wave functions.
344-351
Electronic Edition (link) BibTeX
- Michael Meyer, Alexandre Hocquet, Jürgen Sühnel:
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads.
352-364
Electronic Edition (link) BibTeX
- Pablo Campomanes, María Isabel Menéndez Rodríguez, Ramón López, Tomás Luis Sordo:
Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: A computational study.
365-373
Electronic Edition (link) BibTeX
- Eckart Bindewald, Jeffrey Skolnick:
A scoring function for docking ligands to low-resolution protein structures.
374-383
Electronic Edition (link) BibTeX
- Philippe Carbonniere, Tecla Lucca, Claude Pouchan, Nadia Rega, Vincenzo Barone:
Vibrational computations beyond the harmonic approximation: Performances of the B3LYP density functional for semirigid molecules.
384-388
Electronic Edition (link) BibTeX
- Mehdi Mobli, Raymond J. Abraham:
Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis.
389-398
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Ana Gallegos, Ramon Carbó-Dorca, François Lodier, Eric Cancès, Andreas Savin:
Maximal probability domains in linear molecules.
455-460
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Carlos A. Stortz:
Comparative performance of MM3(92) and two TINKERTM MM3 versions for the modeling of carbohydrates.
471-483
Electronic Edition (link) BibTeX
- Bing Liu, Jiaju Zhou:
SARS-CoV protease inhibitors design using virtual screening method from natural products libraries.
484-490
Electronic Edition (link) BibTeX
- Andrei M. Tokmachev, Andreì L. Tchougréeff:
Transferability of parameters of strictly local geminals' wave function and possibility of sequential derivation of molecular mechanics.
491-505
Electronic Edition (link) BibTeX
- Pierre Tufféry, Frédéric Guyon, Philippe Derreumaux:
Improved greedy algorithm for protein structure reconstruction.
506-513
Electronic Edition (link) BibTeX
Software News & Updates
Volume 26,
Number 6,
April 2005
- Raúl A. Bustos Marún, Eduardo A. Coronado, Juan C. Ferrero:
Fitting complex potential energy surfaces to simple model potentials: Application of the simplex-annealing method.
523-531
Electronic Edition (link) BibTeX
- Vinzenz Bachler:
The behavior of transition metal nitrido bonds towards protonation rationalized by means of localized bonding schemes and their weights.
532-551
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Núria González-García, Àngels González-Lafont, José M. Lluch:
Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH.
569-583
Electronic Edition (link) BibTeX
- Qingyu Kong, Li Zhao, Wenning Wang, Chen Wang, Can Xu, Wingham Zhang, Lei Liu, Kangnian Fan, Yufen Li, Jun Zhuang:
Magic number silicon dioxide-based clusters: Laser ablation-mass spectrometric and density functional theory studies.
584-598
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- T. K. Manojkumar, Chunzhi Cui, Kwang S. Kim:
Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine.
606-611
Electronic Edition (link) BibTeX
- Pedro L. Muiño:
The OH. + CH3SH reaction: Support for an addition-elimination mechanism from ab initio calculations.
612-618
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hong-Qing He, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study for the reaction of CH3OCl with Cl atom.
642-650
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Marcus Lundberg, Per E. M. Siegbahn:
Agreement between experiment and hybrid DFT calculations for OH bond dissociation enthalpies in manganese complexes.
661-667
Electronic Edition (link) BibTeX
- Peter A. Sims, Chung F. Wong, Danka Vuga, James Andrew McCammon, Bartholomew M. Sefton:
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems.
668-681
Electronic Edition (link) BibTeX
- Eric J. Sorin, Vijay S. Pande:
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.
682-690
Electronic Edition (link) BibTeX
- Min-Yi Shen, Karl F. Freed:
A simple method for faster nonbonded force evaluations.
691-698
Electronic Edition (link) BibTeX
- L. Renee Olano, Steven W. Rick:
Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials.
699-707
Electronic Edition (link) BibTeX
- Alán Aspuru-Guzik, Romelia Salomón-Ferrer, Brian Austin, William A. Lester Jr.:
A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo.
708-715
Electronic Edition (link) BibTeX
- Anti Liivat, Alvo Aabloo, John O. Thomas:
Development of a force field for Li2SiF6.
716-724
Electronic Edition (link) BibTeX
- Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren:
An improved nucleic acid parameter set for the GROMOS force field.
725-737
Electronic Edition (link) BibTeX
- Fredrik Blomgren, Sven Larsson:
Exploring the potential energy surface of retinal, a comparison of the performance of different methods.
738-742
Electronic Edition (link) BibTeX
- Neil Gohaud, Didier Bégué, Clovis Darrigan, Claude Pouchan:
New parallel software (P_Anhar) for anharmonic vibrational calculations: Application to (CH3Li)2.
743-754
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Frank J. Owens:
Stability of (C60)2 and epoxide dimers, (C60)2ON, and their anions.
803-806
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Akifumi Oda, Noriyuki Yamaotsu, Shuichi Hirono:
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models.
818-826
Electronic Edition (link) BibTeX
- Alessandro Genoni, Arianna Fornili, Maurizio Sironi:
Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals.
827-835
Electronic Edition (link) BibTeX
- Theodore S. Dibble:
Computations on the A-X transition of isoprene-OH-O2 peroxy radicals.
836-845
Electronic Edition (link) BibTeX
- Jaime Fernández Rico, Ramón López, I. Ema, G. Ramírez:
Translation of STO charge distributions.
846-855
Electronic Edition (link) BibTeX
Software News and Updates
Erratum
Volume 26,
Number 9,
July 2005
- Ia. I. Dobrogorskaia-Méreau, A. V. Nemukhin:
Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion.
865-870
Electronic Edition (link) BibTeX
- Gui-Chang Wang, Jun Li, Xiu-Fang Xu, Rui-Fang Li, Junji Nakamura:
The relationship between adsorption energies of methyl on metals and the metallic electronic properties: A first-principles DFT study.
871-878
Electronic Edition (link) BibTeX
- Andreas Schreiber, Michael Humbert, Alexander Benz, Ursula Dietrich:
3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins.
879-887
Electronic Edition (link) BibTeX
- Per E. M. Siegbahn, Alexander F. Shestakov:
Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase.
888-898
Electronic Edition (link) BibTeX
- Wayne J. Pullan:
An unbiased population-based search for the geometry optimization of Lennard-Jones clusters: 2 leq N leq 372.
899-906
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Art E. Cho, Victor Guallar, Bruce J. Berne, Richard A. Friesner:
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach.
915-931
Electronic Edition (link) BibTeX
- Roberto L. A. Haiduke, Luiz G. M. de Macedo, Albérico B. F. da Silva:
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
Electronic Edition (link) BibTeX
- Illia Horenko, Sönke Lorenz, Christof Schütte, Wilhelm Huisinga:
Adaptive approach for nonlinear sensitivity analysis of reaction kinetics.
941-948
Electronic Edition (link) BibTeX
- Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Structure-breaking effects of solvated Rb(I) in dilute aqueous solution - An ab initio QM/MM MD approach.
949-956
Electronic Edition (link) BibTeX
- Sanjay Banerjee, John A. Board Jr.:
Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics.
957-967
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Chang-Guo Zhan, Shi-Xian Deng, Jaime G. Skiba, Beth A. Hayes, Sarah M. Tschampel, George C. Shields, Donald W. Landry:
First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine.
980-986
Electronic Edition (link) BibTeX
- Toru Inaba, Saisei Tahara, Nobutaka Nisikawa, Hiroshi Kashiwagi, Fumitoshi Sato:
All-electron density functional calculation on insulin with quasi-canonical localized orbitals.
987-993
Electronic Edition (link) BibTeX
- Ying Xue, Chan Kyung Kim, Yong Guo, Daiqian Xie, Guosen Yan:
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
Electronic Edition (link) BibTeX
- G. Theodoor De Jong, Daan P. Geerke, Axel Diefenbach, Miquel Solà, F. Matthias Bickelhaupt:
Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study.
1006-1020
Electronic Edition (link) BibTeX
- Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre:
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms.
1021-1031
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jean-Philip Piquemal, Antonio Marquez, Olivier Parisel, Claude Giessner-Prettre:
A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution.
1052-1062
Electronic Edition (link) BibTeX
- Jerod Parsons, J. Bradley Holmes, J. Maurice Rojas, Jerry Tsai, Charlie E. M. Strauss:
Practical conversion from torsion space to Cartesian space for in silico protein synthesis.
1063-1068
Electronic Edition (link) BibTeX
- Lesley D. Lloyd, Roy L. Johnston, Said Salhi:
Strategies for increasing the efficiency of a genetic algorithm for the structural optimization of nanoalloy clusters.
1069-1078
Electronic Edition (link) BibTeX
- Piotr Zarzycki, Pawel Szabelski, Robert Charmas:
Role of the surface heterogeneity in adsorption of hydrogen ions on metal oxides: Theory and simulations.
1079-1088
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Caterina Benzi, Maurizio Cossi, Roberto Improta, Vincenzo Barone:
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
Electronic Edition (link) BibTeX
- Michael S. Schuurman, Wesley D. Allen, Henry F. Schaefer III:
The ab initio limit quartic force field of BH3.
1106-1112
Electronic Edition (link) BibTeX
- Nohad Gresh, Jean-Philip Piquemal, Morris Krauss:
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
Electronic Edition (link) BibTeX
- Jens Antony, Jean-Philip Piquemal, Nohad Gresh:
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry.
1131-1147
Electronic Edition (link) BibTeX
- Siegfried Höfinger:
Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2.
1148-1154
Electronic Edition (link) BibTeX
- András Perczel, Zoltán Gáspári, Imre G. Csizmadia:
Structure and stability of -pleated sheets.
1155-1168
Electronic Edition (link) BibTeX
- Florian Koskowski, Bernd Hartke:
Towards protein folding with evolutionary techniques.
1169-1179
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hongzhi Li, Yaoqi Zhou:
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation.
1189-1192
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Zexing Cao, Qianer Zhang:
Computational analyses of singlet-singlet and singlet-triplet transitions in mononuclear gold-capped carbon-rich conjugated complexes.
1214-1221
Electronic Edition (link) BibTeX
- Po-Ssu Huang, John J. Love, Stephen L. Mayo:
Adaptation of a fast Fourier transform-based docking algorithm for protein design.
1222-1232
Electronic Edition (link) BibTeX
- Thanh Ha Nguyen, David E. Hibbs, Siân T. Howard:
Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: Implications for the design of synthetic dicarboxylic acid receptors.
1233-1241
Electronic Edition (link) BibTeX
- Andreas W. Götz, Christian Kollmar, Bernd A. Hess:
Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.
1242-1253
Electronic Edition (link) BibTeX
- J. M. Junquera-Hernández, José-Vicente Pitarch Ruiz, José Sánchez-Marín, Stefano Evangelisti, Daniel Maynau:
Multistate active spaces from local CAS-SCF molecular orbitals: The photodissociation of HFCO as an example.
1254-1262
Electronic Edition (link) BibTeX
- Xue-Hai Ju, Xin Wang, Feng-Li Bei:
Substituent effects on heats of formation, group interactions, and detonation properties of polyazidocubanes.
1263-1269
Electronic Edition (link) BibTeX
- Marek Freindorf, Yihan Shao, Thomas R. Furlani, Jing Kong:
Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential.
1270-1278
Electronic Edition (link) BibTeX
- Zhigang Wang, Keyan Lian, Shoufu Pan, Xianhong Fan:
A path from Ih to C1 symmetry for C20 cage molecule.
1279-1283
Electronic Edition (link) BibTeX
- Maria Del Carmen Michelini, Nino Russo, Mohammad Esmaïl Alikhani, Bernard Silvi:
Energetic and topological analyses of the oxidation reaction between Mon (n = 1, 2) and N2O.
1284-1293
Electronic Edition (link) BibTeX
- Christian Bartels, Armin Widmer, Claus Ehrhardt:
Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.
1294-1305
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- David E. Shaw:
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions.
1318-1328
Electronic Edition (link) BibTeX
- Pathumwadee Intharathep, Anan Tongraar, Kritsana Sagarik:
Structure and dynamics of hydrated NH4+: An ab initio QM/MM molecular dynamics simulation.
1329-1338
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- R. Villar, M. J. Gil, J. I. García, V. Martínez-Merino:
Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
1347-1358
Electronic Edition (link) BibTeX
- Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer:
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins.
1359-1371
Electronic Edition (link) BibTeX
- Hitoshi Kusama, Hideki Sugihara:
Theoretical study of quinolines-I2 intermolecular interaction and implications on dye-sensitized solar cell performance.
1372-1382
Electronic Edition (link) BibTeX
- Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann:
A molecular mechanics force field for biologically important sterols.
1383-1399
Electronic Edition (link) BibTeX
- Roberto D. Lins, Philippe H. Hünenberger:
A new GROMOS force field for hexopyranose-based carbohydrates.
1400-1412
Electronic Edition (link) BibTeX
- Youdong Lin, Mark A. Stadtherr:
Deterministic global optimization of molecular structures using interval analysis.
1413-1420
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Gernot Katzer, Alexander F. Sax:
Identification and thermodynamic treatment of several types of large-amplitude motions.
1438-1451
Electronic Edition (link) BibTeX
- Alba T. Macias, Alexander D. MacKerell Jr.:
CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field.
1452-1463
Electronic Edition (link) BibTeX
- Nicholas P. Labello, Antonio M. Ferreira, Henry A. Kurtz:
An augmented effective core potential basis set for the calculation of molecular polarizabilities.
1464-1471
Electronic Edition (link) BibTeX
- Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga:
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
1472-1486
Electronic Edition (link) BibTeX
- Daiqian Xie, Jun Zeng:
Electronic excitations of green fluorescent proteins: Protonation states of chromophore model compound in solutions.
1487-1496
Electronic Edition (link) BibTeX
- A. Patrícia Bento, Miquel Solà, F. Matthias Bickelhaupt:
Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si).
1497-1504
Electronic Edition (link) BibTeX
- Max C. Holthausen:
Benchmarking approximate density functional theory. I. s/d excitation energies in 3d transition metal cations.
1505-1518
Electronic Edition (link) BibTeX
- Bo Liao, Kequan Ding:
Graphical approach to analyzing DNA sequences.
1519-1523
Electronic Edition (link) BibTeX
- Ricardo Oliveira Freire, Gerd Bruno Rocha, Alfredo Mayall Simas:
Modeling lanthanide complexes: Sparkle/AM1 parameters for ytterbium (III).
1524-1528
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 26,
Number 15,
November 2005
- Hui-Yin Wu, Ajay Chaudhari, Shyi-Long Lee:
Theoretical studies on nonlinear optical properties of formaldehyde oligomers by ab initio and density functional theory methods.
1543-1564
Electronic Edition (link) BibTeX
- Jianhan Chen, Wonpil Im, Charles L. Brooks III:
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
1565-1578
Electronic Edition (link) BibTeX
- Maxim Tafipolsky, Rochus Schmid:
Calculation of rotational partition functions by an efficient Monte Carlo importance sampling technique.
1579-1591
Electronic Edition (link) BibTeX
- Chompoonut Rungnim, Vithaya Ruangpornvisuti:
A density functional study of propylene glycol conversion to propanal and propanone of various acid-catalyzed reaction models: A water-addition effect.
1592-1599
Electronic Edition (link) BibTeX
- Yoong-Kee Choe, Shigeru Nagase:
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
Electronic Edition (link) BibTeX
- Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande:
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.
1612-1616
Electronic Edition (link) BibTeX
- Shantenu Jha, Peter V. Coveney, Charles A. Laughton:
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer.
1617-1627
Electronic Edition (link) BibTeX
- Emanuel H. Rubensson, Pawel Salek:
Systematic sparse matrix error control for linear scaling electronic structure calculations.
1628-1637
Electronic Edition (link) BibTeX
- Mark T. Oakley, Jonathan M. Garibaldi, Jonathan D. Hirst:
Lattice models of peptide aggregation: Evaluation of conformational search algorithms.
1638-1646
Electronic Edition (link) BibTeX
- Michael A. Johnston, Ignacio Fdez. Galván, Jordi Villà-Freixa:
Framework-based design of a new all-purpose molecular simulation application: The Adun simulator.
1647-1659
Electronic Edition (link) BibTeX
- G. R. Kneller:
Comment on Using quaternions to calculate RMSD [J. Comp. Chem. 25, 1849 (2004)].
1660-1662
Electronic Edition (link) BibTeX
- Evangelos A. Coutsias, Chaok Seok, Ken A. Dill:
Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller.
1663-1665
Electronic Edition (link) BibTeX
Volume 26,
Number 16,
December 2005
Editorial
- Charles L. Brooks III:
Editorial.
1667
Electronic Edition (link) BibTeX
- David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods:
The Amber biomolecular simulation programs.
1668-1688
Electronic Edition (link) BibTeX
- William L. Jorgensen, Julian Tirado-Rives:
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.
1689-1700
Electronic Edition (link) BibTeX
- David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen:
GROMACS: Fast, flexible, and free.
1701-1718
Electronic Edition (link) BibTeX
- Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren:
The GROMOS software for biomolecular simulation: GROMOS05.
1719-1751
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten:
Scalable molecular dynamics with NAMD.
1781-1802
Electronic Edition (link) BibTeX
Erratum
Copyright © Sun May 17 00:07:18 2009
by Michael Ley (ley@uni-trier.de)
