The dependence of all-atom statistical potentials on structural training database.

ABSTRACT: An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 alpha-proteins and 271 beta-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP (atomic knowledge-based potential), and DFIRE (statistical potential based on distance-scaled finite ideal-gas reference state). These energy functions differ in the reference states used for energy derivation. The energy functions extracted from the different structural databases are used to se

SUBMITTER: Zhang C 

PROVIDER: S-EPMC1304244 | biostudies-literature | 2004 Jun

REPOSITORIES: biostudies-literature