A continuum solvent model: the DISOLV program - algorithms, implementation, and validation

Authors

  • O.Yu. Kupervasser
  • S.N. Zhabin
  • Ya.B. Martynov
  • K.M. Fedulov
  • I.V. Oferkin
  • A.V. Sulimov
  • V.B. Sulimov

Keywords:

polarized continuum model
conductor-like screening model
surface generalized Born model
solvation
implicit solvation model
computer-aided drug design
solvent excluded surface
solvent accessible surface
triangulation
non-polar interactions
polar interactions
force field

Abstract

Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening ��del (COSMO) as well as their implementation in the form of the DISOLV program. The methods for solving the corresponding equations and for computing the analytic gradients are described. The analytic gradients are used for the fast local energy optimization of molecules in a solvent. An algorithm for the original smooth triangulated molecular surface construction is shortly discussed. The procedure for matching the model parameters and the results of the program application to proteins and ligands with the employment of the MMFF94 force field are described. The validation results show the capability of the program to reach a good accuracy (about several tenth of kcal/mol) in the case of the solvation energy calculation for reasonable time periods at arbitrary shifts of the triangulated grid in use for such large molecules as proteins. A good agreement between the calculated and experimentally measured solvation energies in water is obtained with a root-mean-square deviation about 0.8 kcal/mol for several hundreds of molecules.

New computational technologies

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Published

2011-05-16

Issue

Vol. 12 (2011): Issue 2.

Section

Section 1. Numerical methods and applications

Author Biographies

O.Yu. Kupervasser

Lomonosov Moscow State University,
Research Computing Center
• Senior Researcher

S.N. Zhabin

Lomonosov Moscow State University,
Research Computing Center
• Junior Researcher

Ya.B. Martynov

Lomonosov Moscow State University,
Research Computing Center
• Senior Researcher

K.M. Fedulov

Lomonosov Moscow State University,
Research Computing Center
• Programmer

I.V. Oferkin

Lomonosov Moscow State University,
Research Computing Center
• Programmer

A.V. Sulimov

Lomonosov Moscow State University,
Research Computing Center
• System Programmer

V.B. Sulimov

Dimonta, LLC
• Head of Laboratory

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