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JCC
2008
122views more  JCC 2008»
9 years 27 days 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»
9 years 27 days 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»
9 years 1 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
2008
138views more  JCC 2008»
9 years 2 months ago
Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model
Abstract: An increased circular dichroism (CD) signal of large molecular aggregates formed upon DNA condensation was observed a long time ago, and is often referred to as w-CD. The...
Valery Andrushchenko, Petr Bour
JCC
2008
117views more  JCC 2008»
9 years 2 months ago
Prediction of protein structural class using novel evolutionary collocation-based sequence representation
: Knowledge of structural classes is useful in understanding of folding patterns in proteins. Although existing structural class prediction methods applied virtually all state-of-t...
Ke Chen 0003, Lukasz A. Kurgan, Jishou Ruan
JCC
2008
76views more  JCC 2008»
9 years 2 months ago
Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein
Abstract: The dynamic behavior of monomeric Vpu1-32 from HIV-1 in different lipid environments has been studied. The peptide shows highly flexible behavior during the simulations a...
Jens Krüger, Wolfgang B. Fischer
JCC
2008
66views more  JCC 2008»
9 years 2 months ago
Insights on protein-DNA recognition by coarse grain modelling
P. Poulain, A. Saladin, B. Hartmann, C. Pré...
JCC
2008
166views more  JCC 2008»
9 years 2 months ago
Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
: We adapt a combinatorial optimization algorithm, extremal optimization (EO), for the search problem in computational protein design. This algorithm takes advantage of the knowled...
Naigong Zhang, Chen Zeng
JCC
2008
105views more  JCC 2008»
9 years 2 months ago
Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments
Abstract: We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detecte...
Riccardo Chelli, Victor V. Volkov, Roberto Righini
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