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AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling

Authors

  • Emilio Gallicchio,

    Corresponding author
    1. Department of Chemistry and Chemical Biology and BIOMAPS Institute of Quantitative Biology, Rutgers University, Piscataway New Jersey 08854
    • Department of Chemistry and Chemical Biology and BIOMAPS Institute of Quantitative Biology, Rutgers University, Piscataway New Jersey 08854
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  • Ronald M. Levy

    1. Department of Chemistry and Chemical Biology and BIOMAPS Institute of Quantitative Biology, Rutgers University, Piscataway New Jersey 08854
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Abstract

We have developed an implicit solvent effective potential (AGBNP) that is suitable for molecular dynamics simulations and high-resolution modeling. It is based on a novel implementation of the pairwise descreening Generalized Born model for the electrostatic component and a new nonpolar hydration free energy estimator. The nonpolar term consists of an estimator for the solute-solvent van der Waals dispersion energy designed to mimic the continuum solvent solute-solvent van der Waals interaction energy, in addition to a surface area term corresponding to the work of cavity formation. AGBNP makes use of a new parameter-free algorithm to calculate the scaling coefficients used in the pairwise descreening scheme to take into account atomic overlaps. The same algorithm is also used to calculate atomic surface areas. We show that excellent agreement is achieved for the GB self-energies and surface areas in comparison to accurate, but much more expensive, numerical evaluations. The parameter-free approach used in AGBNP and the sensitivity of the AGBNP model with respect to large and small conformational changes makes the model suitable for high-resolution modeling of protein loops and receptor sites as well as high-resolution prediction of the structure and thermodynamics of protein-ligand complexes. We present illustrative results for these kinds of benchmarks. The model is fully analytical with first derivatives and is computationally efficient. It has been incorporated into the IMPACT molecular simulation program. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 479–499, 2004

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