Protein structure statistical database potentials

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

Devising force fields in terms of reduced descriptions of the protein conformation has therefore been a recurring theme in protein computer simulations and structure prediction. It received a new impetus recently with the realization that the body of protein sequence and structure data has probably reached a sufficient size to derive from it effective potentials, which provide an intermediate description between those given by detailed atomic force fields and residue-specific secondary structures. In recent years, a large number of studies has been devoted to this issue.This article reviews these developments, with emphasis on the force fields derived from statistical analyses of known protein structures, also referred to as statistical, database, or knowledge-based potentials. 

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