Database-derived potentials dependent on protein size for in silico folding and design.

ABSTRACT: Knowledge-based potentials are widely used in simulations of protein folding, structure prediction, and protein design. Their advantages include limited computational requirements and the ability to deal with low-resolution protein models compatible with long-scale simulations. Their drawbacks comprehend their dependence on specific features of the dataset from which they are derived, such as the size of the proteins it contains, and their physical meaning is still a subject of debate. We address these issues by probing the theoretical validity of these potentials as mean-force potentials that take the solvent implicitly into account and involve entropic contributions due to atomic degrees of freedom and solvation. The dependence on the size of the system is checked on distance-dependent a

SUBMITTER: Dehouck Y 

PROVIDER: S-EPMC1304340 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature