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    JCC
    2008
    166views more  JCC 2008»
    Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
    13 years 5 months 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
    84views more  JCC 2008»
    Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    13 years 5 months ago
    Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Download  crystal.med.upenn.edu
    : An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Po...
    Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Ki...
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    JCC
    2008
    111views more  JCC 2008»
    Highly accurate biomolecular electrostatics in continuum dielectric environments
    13 years 5 months ago
    Highly accurate biomolecular electrostatics in continuum dielectric environments
    Download  www.mth.msu.edu
    : Implicit solvent models based on the Poisson-Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. ...
    Y. C. Zhou, Michael Feig, G. W. Wei
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    JCC
    2008
    132views more  JCC 2008»
    The implementation of a fast and accurate QM/MM potential method in Amber
    13 years 5 months ago
    The implementation of a fast and accurate QM/MM potential method in Amber
    Download  www.rosswalker.co.uk
    Abstract: Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for...
    Ross C. Walker, Michael F. Crowley, David A. Case
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    JCC
    2008
    114views more  JCC 2008»
    Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter tr
    13 years 5 months ago
    Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter tr
    Download  folding.cnsm.csulb.edu
    Abstract: Molecular dynamics simulations of the RN24 peptide, which includes a diverse set of structurally heterogeneous states, are carried out in explicit solvent. Two approaches...
    Luca Monticelli, Eric J. Sorin, D. Peter Tieleman,...
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