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One‐ and two‐body decomposable Poisson‐Boltzmann methods for protein design calculations
Author(s) -
Marshall Shan A.,
Vizcarra Christina L.,
Mayo Stephen L.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041259105
Subject(s) - side chain , pairwise comparison , poisson–boltzmann equation , computational chemistry , representation (politics) , chemistry , boltzmann constant , statistical physics , polar , physics , chemical physics , molecular physics , biological system , thermodynamics , computer science , quantum mechanics , ion , organic chemistry , artificial intelligence , politics , biology , political science , law , polymer
Successfully modeling electrostatic interactions is one of the key factors required for the computational design of proteins with desired physical, chemical, and biological properties. In this paper, we present formulations of the finite difference Poisson‐Boltzmann (FDPB) model that are pairwise decomposable by side chain. These methods use reduced representations of the protein structure based on the backbone and one or two side chains in order to approximate the dielectric environment in and around the protein. For the desolvation of polar side chains, the two‐body model has a 0.64 kcal/mol RMSD compared to FDPB calculations performed using the full representation of the protein structure. Screened Coulombic interaction energies between side chains are approximated with an RMSD of 0.13 kcal/mol. The methods presented here are compatible with the computational demands of protein design calculations and produce energies that are very similar to the results of traditional FDPB calculations.