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JCC
2008
122views more  JCC 2008»
11 years 5 months ago
Asynchronous replica exchange for molecular simulations
: An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In...
Emilio Gallicchio, Ronald M. Levy, Manish Parashar
JCC
2008
99views more  JCC 2008»
11 years 5 months ago
Assessment of programs for ligand binding affinity prediction
: The prediction of the binding free energy between a ligand and a protein is an important component in the virtual screening and lead optimization of ligands for drug discovery. T...
Ryangguk Kim, Jeffrey Skolnick
JCC
2008
74views more  JCC 2008»
11 years 6 months ago
A study on orientation and absorption spectrum of interfacial molecules by using continuum model
Abstract: In this work, a numerical procedure based on the continuum model is developed and applied to the solvation energy for ground state and the spectral shift against the posi...
Jian-Yi Ma, Jing-Bo Wang, Xiang-Yuan Li, Yao Huang...
JCC
2006
69views more  JCC 2006»
11 years 6 months ago
Dramatic performance enhancements for the FASTER optimization algorithm
: FASTER is a combinatorial optimization algorithm useful for finding low-energy side-chain configurations in side-chain placement and protein design calculations. We present two s...
Benjamin D. Allen, Stephen L. Mayo
JCC
2006
56views more  JCC 2006»
11 years 6 months ago
A comparative theoretical study of dipeptide solvation in water
: Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine
Håkan W. Hugosson, Alessandro Laio, Patrick ...
JCC
2006
78views more  JCC 2006»
11 years 6 months ago
Software news and updates carma: A molecular dynamics analysis program
: A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features s...
Nicholas M. Glykos
JCC
2006
68views more  JCC 2006»
11 years 6 months ago
Relativistic correlating basis sets for lanthanide atoms from Ce to Lu
Masahiro Sekiya, Takeshi Noro, Eisaku Miyoshi, You...
JCC
2006
58views more  JCC 2006»
11 years 6 months ago
On the reversible O2 binding of the Fe-porphyrin complex
: Electronic mechanism of the reversible O2 binding by heme was studied by using Density Functional Theory calculations. The ground state of oxyheme was calculated to be open singl...
Hiroyuki Nakashima, Jun-Ya Hasegawa, Hiroshi Nakat...
JCC
2006
52views more  JCC 2006»
11 years 6 months ago
Transition metal-boron complexes BnM: From bowls (n = 8-14) to tires (n = 14)
Si-Dian Li, Chang-Qing Miao, Jin-Chang Guo, Guang-...
JCC
2006
70views more  JCC 2006»
11 years 6 months ago
SG-0: A small standard grid for DFT quadrature on large systems
: We report the development of a new standard quadrature grid for DFT calculations. Standard Grid 0 (SG-0) is designed to be approximately half as large as, and to provide approxim...
Siu-Hung Chien, Peter M. W. Gill
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