NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures.

ABSTRACT: The current Protein Data Bank (PDB) contains about 40 000 protein structures with approximately half a million incorrect atom positions resulting from erroneously assigned asparagine (Asn) and glutamine (Gln) rotamers. These errors affect applications in protein structure analysis, modeling and docking and therefore the detection, correction and prevention of such errors is highly desirable. We present NQ-Flipper, a web service based on mean force potentials to automatically detect and correct erroneous Asn and Gln rotamers. The service accepts protein structure files formatted in PDB style or PDB codes. For an Asn/Gln side-chain amide NQ-Flipper computes the total interaction energy with the surrounding atoms as the sum of pairwise atom-atom interaction energies. The energy difference bet

SUBMITTER: Weichenberger CX 

PROVIDER: S-EPMC1933125 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature