Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

ABSTRACT:

Background

Protein structure prediction and computational protein design require efficient yet sufficiently accurate descriptions of aqueous solvent. We continue to evaluate the performance of the Coulomb/Accessible Surface Area (CASA) implicit solvent model, in combination with the Charmm19 molecular mechanics force field. We test a set of model parameters optimized earlier, and we also carry out a new optimization in this work, using as a target a set of experimental stability changes for single point mutations of various proteins and peptides. The optimization procedure is general, and could be used with other force fields. The computation of stability changes requires a model for the unfolded state of the protein. In our approach, this state is represented by tripeptide structu

SUBMITTER: am Busch MS 

PROVIDER: S-EPMC2292695 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature