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JCC
2011
109views more  JCC 2011»
12 years 7 months ago
VoteDock: Consensus docking method for prediction of protein-ligand interactions
: Molecular recognition plays a fundamental role in all biological processes, and that is why great efforts have been made to understand and predict protein–ligand interactions. ...
Dariusz Plewczynski, Michal Lazniewski, Marcin von...
JCC
2011
154views more  JCC 2011»
12 years 7 months ago
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
: Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the ...
Dariusz Plewczynski, Michal Lazniewski, Rafal Augu...
JCC
2011
62views more  JCC 2011»
12 years 11 months ago
Paths to which the nudged elastic band converges
Daniel Sheppard, Graeme Henkelman
JCC
2011
87views more  JCC 2011»
12 years 11 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...
JCC
2011
105views more  JCC 2011»
12 years 11 months ago
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Abstract: Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have b...
Michele Seeber, Angelo Felline, Francesco Raimondi...
JCC
2011
55views more  JCC 2011»
12 years 11 months ago
Spin-driven activation of dioxygen in various metalloenzymes and their inspired models
Aurélien de la Lande, Dennis R. Salahub, Ja...
JCC
2011
68views more  JCC 2011»
12 years 11 months ago
Multipole electrostatics in hydration free energy calculations
Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Ren
JCC
2011
133views more  JCC 2011»
12 years 11 months ago
MIBPB: A software package for electrostatic analysis
: The Poisson–Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the soluti...
Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng, ...
JCC
2011
91views more  JCC 2011»
12 years 11 months ago
Nucleic acid sequence design via efficient ensemble defect optimization
Joseph N. Zadeh, Brian R. Wolfe, Niles A. Pierce