PUDGE: A flexible, interactive server for protein structure prediction

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Norel, Raquel ^a   Petrey, Donald ^a   Honig, Barry ^a  

^a Center for Computational Biology and Bioinformatics Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; WEB BROWSER; CHEMICAL STRUCTURE; CHEMISTRY; INTERNET; STRUCTURAL HOMOLOGY;

BACTERIAL PROTEINS; INTERNET; MODELS, MOLECULAR; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

BACTERIAL PROTEIN;

EID: 77954249072     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq475     Document Type: Article

References (22)

1. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
2. Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
3. Dosztanyi,Z., Csizmok,V., Tompa,P. and Simon,I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
4. Petrey,D., Fischer,M. and Honig,B. (2009) Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc. Natl Acad. Sci. USA, 106, 17377-17382.
5. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
6. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
7. Petrey,D., Xiang,Z., Tang,C.L., Xie,L., Gimpelev,M., Mitros,T., Soto,C.S., Goldsmith-Fischman,S., Kernytsky,A., Schlessinger,A. et al. (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins, 53(Suppl. 6), 430-435.
8. Tang,C.L., Xie,L., Koh,I.Y., Posy,S., Alexov,E. and Honig,B. (2003) On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J. Mol. Biol., 334, 1043-1062.
9. Xiang,Z. and Honig,B. (2001) Extending the accuracy limits of prediction for side-chain conformations. J. Mol. Biol., 311, 421-430.
10. Bowie,J.U., Luthy,R. and Eisenberg,D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
11. Luthy,R., Bowie,J.U. and Eisenberg,D. (1992) Assessment of protein models with 3-dimensional profiles. Nature, 356, 83-85.
12. 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.
13. de Matos,P., Alcantara,R., Dekker,A., Ennis,M., Hastings,J., Haug,K., Spiteri,I., Turner,S. and Steinbeck,C. (3000) Chemical entities of biological interest: an update. Nucl. Acids Res., 38, D249-254.
14. Degtyarenko,K., de Matos,P., Ennis,M., Hastings,J., Zbinden,M., McNaught,A., Alcantara,R., Darsow,M., Guedj,M. and Ashburner,M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucl. Acids Res., 36, D344-350.
15. Degtyarenko,K., Hastings,J., de Matos,P. and Ennis,M. (2009) ChEBI: an open bioinformatics and cheminformatics resource. Curr. Protoc. Bioinformatics, Chapter 14, Unit 14.19.
16. Sippl,M.J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355-362.
17. Yu,S., Jensen,V., Seeliger,J., Feldmann,I., Weber,S., Schleicher,E., Häussler,S. and Blankenfeldt,W. (2009) Structure elucidation and preliminary assessment of hydrolase activity of PqsE, the Pseudomonas quinolone signal (PQS) response protein. Biochemistry, 48, 10298-10307.
18. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
19. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
20. Jacobson,M.P., Friesner,R.A., Xiang,Z. and Honig,B. (2002) On the role of the crystal environment in determining protein side-chain conformations. J. Mol. Biol., 320, 597-608.
21. Xiang,Z., Soto,C.S. and Honig,B. (2002) Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc. Natl Acad. Sci. USA, 99, 7432-7437.
22. Canutescu,A.A., Shelenkov,A.A. and Dunbrack,R.L. Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.