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TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives
[Image: see text] We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called T...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2014
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159216/ https://www.ncbi.nlm.nih.gov/pubmed/25221446 http://dx.doi.org/10.1021/ct5002818 |
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author | Drechsel, Nils J. D. Fennell, Christopher J. Dill, Ken A. Villà-Freixa, Jordi |
author_facet | Drechsel, Nils J. D. Fennell, Christopher J. Dill, Ken A. Villà-Freixa, Jordi |
author_sort | Drechsel, Nils J. D. |
collection | PubMed |
description | [Image: see text] We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called TRIFORCE, reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application. |
format | Online Article Text |
id | pubmed-4159216 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-41592162015-07-23 TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives Drechsel, Nils J. D. Fennell, Christopher J. Dill, Ken A. Villà-Freixa, Jordi J Chem Theory Comput [Image: see text] We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called TRIFORCE, reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application. American Chemical Society 2014-07-23 2014-09-09 /pmc/articles/PMC4159216/ /pubmed/25221446 http://dx.doi.org/10.1021/ct5002818 Text en Copyright © 2014 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) |
spellingShingle | Drechsel, Nils J. D. Fennell, Christopher J. Dill, Ken A. Villà-Freixa, Jordi TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives |
title | TRIFORCE:
Tessellated Semianalytical Solvent Exposed
Surface Areas and Derivatives |
title_full | TRIFORCE:
Tessellated Semianalytical Solvent Exposed
Surface Areas and Derivatives |
title_fullStr | TRIFORCE:
Tessellated Semianalytical Solvent Exposed
Surface Areas and Derivatives |
title_full_unstemmed | TRIFORCE:
Tessellated Semianalytical Solvent Exposed
Surface Areas and Derivatives |
title_short | TRIFORCE:
Tessellated Semianalytical Solvent Exposed
Surface Areas and Derivatives |
title_sort | triforce:
tessellated semianalytical solvent exposed
surface areas and derivatives |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159216/ https://www.ncbi.nlm.nih.gov/pubmed/25221446 http://dx.doi.org/10.1021/ct5002818 |
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