Toward better refinement of comparative models: predicting loops in inexact environments.

ABSTRACT: Achieving atomic-level accuracy in comparative protein models is limited by our ability to refine the initial, homolog-derived model closer to the native state. Despite considerable effort, progress in developing a generalized refinement method has been limited. In contrast, methods have been described that can accurately reconstruct loop conformations in native protein structures. We hypothesize that loop refinement in homology models is much more difficult than loop reconstruction in crystal structures, in part, because side-chain, backbone, and other structural inaccuracies surrounding the loop create a challenging sampling problem; the loop cannot be refined without simultaneously refining adjacent portions. In this work, we single out one sampling issue in an artificial but useful tes

SUBMITTER: Sellers BD 

PROVIDER: S-EPMC2764870 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature