Fourier transform convolution integrals applied to generalized Born molecular volume.

Details

Serval ID
serval:BIB_DC2794DC7801
Type
Article: article from journal or magazin.
Publication sub-type
Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.
Collection
Publications
Institution
Title
Fourier transform convolution integrals applied to generalized Born molecular volume.
Journal
Journal of Computational Chemistry
Author(s)
Schüpbach T., Zoete V., Tsakam-Sotché B., Michielin O.
ISSN
1096-987X[electronic], 0192-8651[linking]
Publication state
Published
Issued date
2010
Volume
31
Number
3
Pages
649-659
Language
english
Abstract
Generalized Born methods are currently among the solvation models most commonly used for biological applications. We reformulate the generalized Born molecular volume method initially described by (Lee et al, 2003, J Phys Chem, 116, 10606; Lee et al, 2003, J Comp Chem, 24, 1348) using fast Fourier transform convolution integrals. Changes in the initial method are discussed and analyzed. Finally, the method is extensively checked with snapshots from common molecular modeling applications: binding free energy computations and docking. Biologically relevant test systems are chosen, including 855-36091 atoms. It is clearly demonstrated that, precision-wise, the proposed method performs as good as the original, and could better benefit from hardware accelerated boards.
Keywords
Algorithms, Fourier Analysis, Molecular Dynamics Simulation, Solvents/chemistry, Thermodynamics, Trypsin/chemistry
Pubmed
Web of science
Create date
08/01/2010 14:46
Last modification date
20/08/2019 16:01
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