NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures.
The error rate of asparagine (Asn) and glutamine (Gln) amide rotamers in protein crystal structures is in the order of 20% and as a consequence the current Protein Database (PDB) contains approximately half a million incorrect Asn and Gln side-chain rotamers. Here we present NQ-Flipper, a web service based on knowledge-based potentials of mean force to automatically detect and correct erroneous rotamers. We achieve excellent agreement with expert curated data.
Weichenberger
Christian X
CX
Center of Applied Molecular Engineering, University of Salzburg, Jakob Haringerstrasse 5, 5020 Salzburg, Austria.
Sippl
Manfred J
MJ
D001216:Asparagine / Q000737:chemistry*; D003461:Crystallography / Q000379:methods*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D005973:Glutamine / Q000737:chemistry*; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D017510:Protein Folding; D015203:Reproducibility of Results; D012984:Software; D013816:Thermodynamics
D005973:Glutamine; D001216:Asparagine