Fourier transform convolution integrals applied to generalized Born molecular volume.
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.
Schüpbach
Thierry
T
Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland. thierry.schuepbach@isb-sib.ch
Zoete
Vincent
V
Tsakam-Sotché
Brice
B
Michielin
Olivier
O
D000465:Algorithms; D005583:Fourier Analysis; D056004:Molecular Dynamics Simulation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry*
D012997:Solvents; D014357:Trypsin