A supersecondary structure library and search algorithm for modeling loops in protein structures.

ABSTRACT: We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by th

SUBMITTER: Fernandez-Fuentes N 

PROVIDER: S-EPMC1440879 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature