Joint neighbors approximation of macromolecular solvent accessible surface area
- PMID: 17407094
- DOI: 10.1002/jcc.20550
Joint neighbors approximation of macromolecular solvent accessible surface area
Abstract
A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 A2, while for unfolded protein conformations it varies from 1.65 to 1.87 A2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today.
Copyright 2007 Wiley Periodicals, Inc.
Similar articles
-
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.J Comput Chem. 2004 Jun;25(8):1005-14. doi: 10.1002/jcc.20026. J Comput Chem. 2004. PMID: 15067676
-
Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities.Biopolymers. 1999 Oct 5;50(4):373-80. doi: 10.1002/(SICI)1097-0282(19991005)50:4<373::AID-BIP3>3.0.CO;2-U. Biopolymers. 1999. PMID: 10423546
-
Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.J Comput Chem. 2002 Jan 30;23(2):214-21. doi: 10.1002/jcc.1167. J Comput Chem. 2002. PMID: 11924735
-
A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states.Curr Protein Pept Sci. 2014;15(5):456-76. doi: 10.2174/1389203715666140327114232. Curr Protein Pept Sci. 2014. PMID: 24678666 Review.
-
Hollow crescents, helices, and macrocycles from enforced folding and folding-assisted macrocyclization.Acc Chem Res. 2008 Oct;41(10):1376-86. doi: 10.1021/ar700266f. Epub 2008 May 7. Acc Chem Res. 2008. PMID: 18459803 Review.
Cited by
-
Slow, reversible, coupled folding and binding of the spectrin tetramerization domain.Biophys J. 2012 Nov 21;103(10):2203-14. doi: 10.1016/j.bpj.2012.10.012. Epub 2012 Nov 20. Biophys J. 2012. PMID: 23200054 Free PMC article.
-
Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains.Nat Commun. 2024 May 20;15(1):4283. doi: 10.1038/s41467-024-48487-8. Nat Commun. 2024. PMID: 38769318 Free PMC article.
-
Generating triangulated macromolecular surfaces by Euclidean Distance Transform.PLoS One. 2009 Dec 2;4(12):e8140. doi: 10.1371/journal.pone.0008140. PLoS One. 2009. PMID: 19956577 Free PMC article.
-
Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer.Biochemistry. 2012 Jan 10;51(1):565-72. doi: 10.1021/bi201642p. Epub 2011 Dec 16. Biochemistry. 2012. PMID: 22192051 Free PMC article.
-
On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.J Chem Theory Comput. 2011 Nov 1;7(11):3608-3619. doi: 10.1021/ct200389p. J Chem Theory Comput. 2011. PMID: 24772042 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
