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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 4 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
    88views more  JCC 2008»
    A self-organizing algorithm for molecular alignment and pharmacophore development
    13 years 4 months ago
    A self-organizing algorithm for molecular alignment and pharmacophore development
    Download  www.dimitris-agrafiotis.com
    Abstract: We present a method for simultaneous three-dimensional (3D) structure generation and pharmacophorebased alignment using a self-organizing algorithm called Stochastic Prox...
    Deepak Bandyopadhyay, Dimitris K. Agrafiotis
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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 4 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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    JCC
    2008
    131views more  JCC 2008»
    An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations
    13 years 4 months ago
    An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations
    Download  www.wag.caltech.edu
    : Quantum Monte Carlo (QMC) calculations require the generation of random electronic configurations with respect to a desired probability density, usually the square of the magnitu...
    Daniel R. Fisher, David R. Kent IV, Michael T. Fel...
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    JCC
    2008
    125views more  JCC 2008»
    Efficient electronic integrals and their generalized derivatives for object oriented implementations of electronic structure cal
    13 years 4 months ago
    Efficient electronic integrals and their generalized derivatives for object oriented implementations of electronic structure cal
    Download  www.qtp.ufl.edu
    : For the new parallel implementation of electronic structure methods in ACES III (Lotrich et al., in preparation) the present state-of-the-art algorithms for the evaluation of ele...
    Norbert Flocke, Victor Lotrich
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    JCC
    2008
    76views more  JCC 2008»
    Effects of spin-orbit coupling on magnetic properties of discrete and extended magnetic systems
    13 years 4 months ago
    Effects of spin-orbit coupling on magnetic properties of discrete and extended magnetic systems
    Download  www4.ncsu.edu
    : In accounting for the magnetic properties of discrete and extended compounds with unpaired spins, it is crucial to know the nature of their ground and low-lying excited states. I...
    Dadi Dai, Hongjun Xiang, Myung-Hwan Whangbo
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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 4 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
    91views more  JCC 2008»
    An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
    13 years 4 months ago
    An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
    Download  www.mayo.caltech.edu
    Abstract: Our goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously ...
    Christina L. Vizcarra, Naigong Zhang, Shannon A. M...
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    JCC
    2008
    117views more  JCC 2008»
    FACTS: Fast analytical continuum treatment of solvation
    13 years 4 months ago
    FACTS: Fast analytical continuum treatment of solvation
    Download  www.biochem-caflisch.unizh.ch
    : An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation...
    Urs Haberthür, Amedeo Caflisch
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    JCC
    2008
    92views more  JCC 2008»
    Fast procedure for reconstruction of full-atom protein models from reduced representations
    13 years 4 months ago
    Fast procedure for reconstruction of full-atom protein models from reduced representations
    Download  cssb.biology.gatech.edu
    : We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly su...
    Piotr Rotkiewicz, Jeffrey Skolnick
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