Paper Info
Title
A rapid solvent accessible surface area estimator for coarse grained molecular simulations.
Abstract
The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on C-only protein structures. Through an extensive comparison between this method and a comparable method, POPS-R, we demonstrate that our new method, Protein-C Solvent Accessibilities or PCASA, shows better performance, especially for unfolded conformations of proteins. We anticipate that this model will be quite useful in the efficient inclusion of SASA-based solvent free energy estimations in coarse-grained protein folding simulations. PCASA is made freely available to the academic community at . (c) 2017 Wiley Periodicals, Inc.
Year
DOI
Venue
2017
10.1002/jcc.24709
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
residue-wise SASA,go-model,coarse-grained protein structure,Bayesian linear regression
Protein folding,Sasa,Computational chemistry,Chemistry,Accessible surface area,Solvent models,Solvation,Biophysical Process,Academic community,Estimator
Journal
Volume
Issue
ISSN
38.0
15
0192-8651
Citations 
PageRank 
References 
1
0.35
8
Authors
3
Name
Order
Citations
PageRank
Shuai Wei110.35
Charles L. Brooks III21198126.06
Aaron T. Frank321.71