Format

Send to

Choose Destination
J Chem Theory Comput. 2014 Sep 9;10(9):4121-4132. Epub 2014 Jul 23.

TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives.

Author information

1
Computational Biochemistry and Biophysics Laboratory, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra , C/Doctor Aiguader, 88, 08003 Barcelona, Catalunya, Spain ; Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794-5252, United States ; Department of Chemistry, Oklahoma State University , Stillwater, Oklahoma 74078, United States.
2
Department of Chemistry, Oklahoma State University , Stillwater, Oklahoma 74078, United States.
3
Laufer Center for Physical and Quantitative Biology and Departments of Physics and Chemistry, Stony Brook University , Stony Brook, New York 11794-5252, United States.
4
Computational Biochemistry and Biophysics Laboratory, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra , C/Doctor Aiguader, 88, 08003 Barcelona, Catalunya, Spain ; Escola Politècnica Superior, Universitat de Vic-Universitat Central de Catalunya , C/de la Laura, 13, 08500 Vic, Catalunya, Spain.

Abstract

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.

Supplemental Content

Full text links

Icon for PubMed Central
Loading ...
Support Center