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Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.

ABSTRACT: We propose a pairwise and readily parallelizable SASA-based nonpolar solvation approach for protein simulations, inspired by our previous pairwise GB polar solvation model development. In this work, we developed a novel function to estimate the atomic and molecular SASAs of proteins, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values. Implemented in Amber software and tested on consumer GPUs, our pwSASA method reasonably reproduces LCPO simulation results, but accelerates MD simulations up to 30 times compared to the LCPO implementation, which is greatly desirable for protein simulations facing sampling challenges. The value of incorporating the nonpolar term in implicit solvent simulations is explored on a peptide fragment containing the hydrophobic core of HP36 and evaluating thermal stability profiles of four small proteins.

SUBMITTER: Huang H

PROVIDER: S-EPMC6600810 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.

Huang He H Simmerling Carlos C

Journal of chemical theory and computation 20181025 11

We propose a pairwise and readily parallelizable SASA-based nonpolar solvation approach for protein simulations, inspired by our previous pairwise GB polar solvation model development. In this work, we developed a novel function to estimate the atomic and molecular SASAs of proteins, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values. Implemented in Amber software and tested on consumer GPUs, our pwSASA method reasonably reproduces L ...[more]

PMID: 30303377

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