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    JCC
    2008
    122views more  JCC 2008»
    Asynchronous replica exchange for molecular simulations
    13 years 11 months ago
    Asynchronous replica exchange for molecular simulations
    Download  hpcp.rutgers.edu
    : 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
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    JCC
    2008
    99views more  JCC 2008»
    Assessment of programs for ligand binding affinity prediction
    13 years 11 months ago
    Assessment of programs for ligand binding affinity prediction
    Download  cssb.biology.gatech.edu
    : 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
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    JCC
    2008
    74views more  JCC 2008»
    A study on orientation and absorption spectrum of interfacial molecules by using continuum model
    14 years 2 days ago
    A study on orientation and absorption spectrum of interfacial molecules by using continuum model
    Download  ccg.scu.edu.cn
    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...
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    JCC
    2008
    138views more  JCC 2008»
    Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model
    14 years 17 days ago
    Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model
    Download  hanicka.uochb.cas.cz
    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
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    JCC
    2008
    64views more  JCC 2008»
    Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
    14 years 17 days ago
    Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
    Download  cssb.biology.gatech.edu
    Michal Brylinski, Jeffrey Skolnick
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    JCC
    2008
    117views more  JCC 2008»
    Prediction of protein structural class using novel evolutionary collocation-based sequence representation
    14 years 17 days ago
    Prediction of protein structural class using novel evolutionary collocation-based sequence representation
    Download  biomine.ece.ualberta.ca
    : 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
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    JCC
    2008
    76views more  JCC 2008»
    Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein
    14 years 17 days ago
    Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein
    Download  www.ym.edu.tw
    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
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    JCC
    2008
    66views more  JCC 2008»
    Insights on protein-DNA recognition by coarse grain modelling
    14 years 17 days ago
    Insights on protein-DNA recognition by coarse grain modelling
    Download  www.dsimb.inserm.fr
    P. Poulain, A. Saladin, B. Hartmann, C. Pré...
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    JCC
    2008
    166views more  JCC 2008»
    Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
    14 years 17 days ago
    Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
    Download  home.gwu.edu
    : 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
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    JCC
    2008
    105views more  JCC 2008»
    Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments
    14 years 17 days ago
    Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments
    Download  www.chim.unifi.it
    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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