NQ-Flipper: Validation and correction of asparagine/glutamine amide rotamers in protein crystal structures

Bioinformatics

Volumn 22, Issue 11, 2006, Pages 1397-1398

  Weichenberger, Christian X ^a   Sippl, Manfred J ^a  

^a UNIVERSITY OF SALZBURG   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; ASPARAGINE; GLUTAMINE;

ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; VALIDATION PROCESS;

EID: 33745599120     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl128     Document Type: Article

References (7)

1. Baldi,P. et al. (2000) Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 16, 412-424.
2. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
3. Hooft,R.W. et al. (1996) Errors in protein structures. Nature, 381, 272.
4. Lovell,S.C. et al. (2003) Structure validation by Calpha geometry: Phi, psi and Cbeta deviation. Proteins, 50, 437-450.
5. McDonald,I.K. and Thornton,J.M. (1995) The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains. Protein Eng., 8, 217-224.
6. Sippl,M.J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol., 213, 859-883.
7. Word,J.M. et al. (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285, 1735-1747.