Modeling Proteins Conformation in Solution. Part II: A Solvent Effect Model Based on the Evaluation of Solvent-Accessible Surface Area and Generalized Born Equation

Valentin Gogonea [1] (
Camelia Baleanu-Gogonea [2] (
Carlos A. Del Carpio [3] (

[1] Computer Chemistry Center, Institute for Organic Chemistry
Erlangen-Nurnberg University, Nagelsbachstr.
25, D-91052 Erlangen, Germany
[2] Laboratory of Molecular Biology,
Department of Ecological Engineering.
Toyohashi University of Technology.
Tempaku, Toyohashi 441, Japan
[3] Laboratory for Informatics & AI in Molecular and Biological Sciences Department of Ecological Engineering,
Toyohashi University of Technology.
Tempaku. Toyohashi 441, Japan


This is the second of a series of articles describing our system for prediction of protein conformation in solution. Here we propose a force field for studying protein folding in solution. Our force field is made up of an internal force field (MM2) and a solvent force field which sums up the constrains that solvent imposes to protein structure in solution, as compared with the gas phase.