Gaia: Automated quality assessment of protein structure models

Bioinformatics

Volumn 27, Issue 16, 2011, Pages 2209-2215

  Kota, Pradeep ^a,b   Ding, Feng ^a,b   Ramachandran, Srinivas ^a,b   Dokholyan, Nikolay V ^a,b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN CONFORMATION;

MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 79961202365     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr374     Document Type: Article

References (20)

1. Busa,J. et al. (2010) CAVE: a package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins. Comput. Phys. Commun., 181, 2116-2125.
2. Bystroff,C. (2002) MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. Protein Eng., 15, 959-965.
3. Connolly,M. (1983) Analytical molecular surface calculation. J. Appl. Crystallogr., 16, 548-558.
4. Cuff,A.L. and Martin,A.C. (2004) Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein, J. Mol. Biol., 344, 1199-1209.
5. Davis,I.W. et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res., 35, W375-W383.
6. Ding,F. and Dokholyan,N.V. (2006) Emergence of protein fold families through rational design. PLoS Comput. Biol., 2, e85.
7. Dunbrack,R.L. Jr. and Cohen,F.E. (1997) Bayesian statistical analysis of protein sidechain rotamer preferences. Protein Sci., 6, 1661-1681.
8. Eriksson,A.E. et al. (1992) Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science, 255, 178-183.
9. Fleming,P.J. and Rose,G.D. (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci., 14, 1911-1917.
10. Hooft,R.W.W. et al. (1996) Errors in protein structures. Nature, 381, 272-272.
11. Joosten,R.P. et al. (2009) PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J. Appl. Crystallogr., 42, 376-384.
12. Kleywegt,G.J. and Jones,T.A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta. Crystallogr. D., 50, 178-185.
13. Laskowski,R.A. et al. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
14. Le Grand,S.M. and Merz,K.M.J. (1993) Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. J. Comput. Chem., 14, 349-352.
15. Liang,J. et al. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884-1897.
16. Ramachandran,G.N. et al. (1963) Stereochemistry of polypeptide chain configurations. J. Mol. Biol., 7, 95-99.
17. Ramachandran,S. et al. (2011) Automated minimization of steric clashes in protein structures. Proteins: Struct. Funct. Bioinf., 79, 261-270.
18. Sanner,M.F. et al. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38, 305-320.
19. Vriend,G. and Sander,C. (1993) Quality control of protein models: directional atomic contact analysis. J. Appl. Cryst., 26, 47-60.
20. Yin,S. et al. (2007) Modeling backbone flexibility improves protein stability estimation. Structure, 15, 1567-1576.