Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.

ABSTRACT: Misfit sidechains in protein crystal structures are a stumbling block in using those structures to direct further scientific inference. Problems due to surface disorder and poor electron density are very difficult to address, but a large class of systematic errors are quite common even in well-ordered regions, resulting in sidechains fit backwards into local density in predictable ways. The MolProbity web site is effective at diagnosing such errors, and can perform reliable automated correction of a few special cases such as 180 degrees flips of Asn or Gln sidechain amides, using all-atom contacts and H-bond networks. However, most at-risk residues involve tetrahedral geometry, and their valid correction requires rigorous evaluation of sidechain movement and sometimes backbone shift. The c

SUBMITTER: Headd JJ 

PROVIDER: S-EPMC2704614 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature