QMEAN server for protein model quality estimation

Nucleic Acids Research

Volumn 37, Issue SUPPL. 2, 2009, Pages

  Benkert, Pascal ^a,b   Künzli, Michael ^a,b   Schwede, Torsten ^a,b  

^a UNIVERSITY OF BASEL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN STRUCTURE; RELIABILITY; SCORING SYSTEM; STRUCTURE ANALYSIS; WEB BROWSER;

MODELS, MOLECULAR; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 67650358909     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp322     Document Type: Article

References (32)

1. Chen,H. and Kihara,D. (2008) Estimating quality of template-based protein models by alignment stability. Proteins, 71, 1255-1274.
2. Tress,M.L., Jones,D. and Valencia,A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol., 330, 705-718.
3. Sippl,M.J. (1993) Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comput. Aided Mol. Des., 7, 473-501.
4. Ramachandran,G.N., Ramakrishnan,C. and Sasisekharan,V. (1963) Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95-99.
5. Melo,F. and Feytmans,E. (1997) Novel knowledge-based mean force potential at atomic level. J. Mol. Biol., 267, 207-222.
6. Benkert,P., Tosatto,S.C.E. and Schomburg,D. (2008) QMEAN: A comprehensive scoring function for model quality assessment. Prot. Struct. Funct. Bioinformatics, 71, 261-277.
7. Tosatto,S. (2005) The victor/FRST function for model quality estimation. J. Comput. Biol.: J. Comput. Mol. Cell Biol., 12, 1316-1327.
8. Zhou,H. and Zhou,Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
9. Samudrala,R. and Moult,J. (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol., 275, 895-916.
10. Luthy,R., Bowie,J.U. and Eisenberg,D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
11. Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
12. Lundstrom,J., Rychlewski,L., Bujnicki,J. and Elofsson,A. (2001) Pcons: A neural-network-based consensus predictor that improves fold recognition. Protein Sci., 10, 2354-2362.
13. McGuffin,L.J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics, 8, 345.
14. Moult,J., Fidelis,K., Kryshtafovych,A., Rost,B., Hubbard,T. and Tramontano,A. (2007) Critical assessment of methods of protein structure prediction - Round VII. Prot. Struct., Funct. Bioinformatics, 69, 3-9.
15. Cozzetto,D., Kryshtafovych,A., Ceriani,M. and Tramontano,A. (2007) Assessment of predictions in the model quality assessment category. Proteins, 69 (Suppl. 8), 175-183.
16. Kurowski,M.A. and Bujnicki,J.M. (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res., 31, 3305-3307.
17. Wallner,B., Fang,H. and Elofsson,A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins, 53 (Suppl. 6), 534-541.
18. Rohl,C.A., Strauss,C.E., Misura,K.M. and Baker,D. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
19. Wu,S., Skolnick,J. and Zhang,Y. (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol., 5, 17.
20. McGuffin,L.J. (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics, 24, 586-587.
21. Wallner,B. and Elofsson,A. (2003) Can correct protein models be identified? Protein Sci., 12, 1073-1086.
22. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
23. Cheng,J., Randall,A.Z., Sweredoski,M.J. and Baldi,P. (2005) SCRATCH: A protein structure and structural feature prediction server. Nucleic Acids Res., 33, W72-W76.
24. Wallner,B. and Elofsson,A. (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins, 69 (Suppl. 8) 184-193.
25. Zemla,A. (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
26. Bordoli,L., Kiefer,F., Arnold,K., Benkert,P., Battey,J. and Schwede,T. (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protoc., 4, 1-13.
27. Arnold,K., Bordoli,L., Kopp,J. and Schwede,T. (2006) The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201.
28. Wallner,B. and Elofsson,A. (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci., 15, 900-913.
29. Melo,F., Devos,D., Depiereux,E. and Feytmans,E. (1997) ANOLEA: A www server to assess protein structures. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 187-190.
30. Hooft,R.W., Vriend,G., Sander,C. and Abola,E.E. (1996) Errors in protein structures. Nature, 381, 272.
31. Kiefer,F., Arnold,K., Kunzli,M., Bordoli,L. and Schwede,T. (2009) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. 37, D387-D392.
32. Benkert,P., Tosatto,S. and Schwede,T. (2009) Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins, Suppl, in press.