Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.

ABSTRACT:

Background

Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose.

Results

We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS), which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with

SUBMITTER: Rakhmanov SV 

PROVIDER: S-EPMC1852318 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature