Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

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Scalable free energy calculation of proteins via multiscale essential sampling

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Continuous surface charge polarizable continuum models of solvation. I. General formalism

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Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

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Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

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Calculation of the electrostatic charges and energies for intercalation of aromatic drug molecules with DNA

(2009) V. V. Kostjukov et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin

(2009) L. Ramya et al.   Journal of Chemical Theory and Computation

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

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A Minima Hopping Study of All-Atom Protein Folding and Structure Prediction

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Reversible folding simulation by hybrid Hamiltonian replica exchange

(2008) Weixin Xu et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models

(2008) Lixin Zhan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

FOLDING FREE ENERGY LANDSCAPE OF THE DECAPEPTIDE CHIGNOLIN

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Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation

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