Modeling of loops in proteins: a multi-method approach.

ABSTRACT:

Background

Template-target sequence alignment and loop modeling are key components of protein comparative modeling. Short loops can be predicted with high accuracy using structural fragments from other, not necessairly homologous proteins, or by various minimization methods. For longer loops multiscale approaches employing coarse-grained de novo modeling techniques should be more effective.

Results

For a representative set of protein structures of various structural classes test predictions of loop regions have been performed using MODELLER, ROSETTA, and a CABS coarse-grained de novo modeling tool. Loops of various length, from 4 to 25 residues, were modeled assuming an ideal target-template alignment of the remaining portions of the protein. It has been shown that classical

SUBMITTER: Jamroz M 

PROVIDER: S-EPMC2837870 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature