ArticleJournal of chemical theory and computation2018
Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed.
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- Selection of short Gadd45β-binding peptides through a synergistic computational and biophysical approach.Protein science : a publication of the Protein Society · 2025Article
- Chaperone-mediated thermotolerance in hyperthermophilic composting: Molecular-Level protein remodeling of microbial communities.Environmental science and ecotechnology · 2025Article
- Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials.The journal of physical chemistry. B · 2025Article
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Coarse-Grained Simulation Study of the Association of Selected Dipeptides.The journal of physical chemistry. B · 2024Article
- From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.Journal of chemical theory and computation · 2024Article
- Article
- Molecular dynamics simulations as a guide for modulating small molecule aggregation.Journal of computer-aided molecular design · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
- Elucidation of Molecular Interactions Between Drug-Polymer in Amorphous Solid Dispersion by a Computational Approach Using Molecular Dynamics Simulations.Advances and applications in bioinformatics and chemistry : AABC · 2024Article
- Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.The journal of physical chemistry. B · 2022Article
- Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets ofRSC advances · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.