Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Zhou, Hongyi ^a   Zhang, Chi ^a   Liu, Song ^a   Zhou, Yaoqi ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN; MUTANT PROTEIN; AMINO ACID; VEGETABLE PROTEIN; DNA; MONOMER;

ARTICLE; BINDING AFFINITY; CLIENT SERVER APPLICATION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA PROTEIN COMPLEX; ENERGY TRANSFER; INTERNET; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PHASE TRANSITION; PLANT; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SPECIES COMPARISON; CHEMISTRY; COMPUTER PROGRAM; KINETICS; SEQUENCE ANALYSIS; BINDING KINETICS; COMPLEX FORMATION; COMPUTER PREDICTION; DNA TEMPLATE; ENERGY; MUTANT; ORGANISM;

AMINO ACIDS; INTERNET; KINETICS; MARKOV CHAINS; MEMBRANE PROTEINS; PLANT PROTEINS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 23144454057     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki360     Document Type: Article

References (32)

1. Zhou,H. and Zhou,Y. (2003) Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci., 12, 1547-1555.
2. Zhou,H. and Zhou,Y. (2004) Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins, 55, 1005-1013.
3. Zhou,H. and Zhou,Y. (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins, 58, 321-328.
4. 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.
5. Zhang,C., Liu,S. and Zhou,Y. (2004) Accurate and efficient loop selections using DFIRE-based all-atom statistical potential. Protein Sci., 13, 391-399.
6. Liu,S., Zhang,C., Zhou,H. and Zhou,Y. (2004) A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins, 56, 93-101.
7. Zhang,C., Liu,S., Zhu,Q. and Zhou,Y. (2005) A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes. J. Med. Chem. in press.
8. Zhou,H. and Zhou,Y. (2002) Folding rate prediction using total contact distance. Biophys. J., 82, 458-463.
9. Bai,Y., Zhou,H. and Zhou,Y. (2004) Critical nucleation size in the folding of small apparently two-state proteins. Protein Sci., 13, 1173-1181.
10. Liu,S., Zhang,C. and Zhou,Y. (2005) Domains and domain combinations in Arabidopsis thaliana by comparative analysis. J. Proteome Res., in press.
11. Eisenberg,D., Weiss,R.M., Terwilliger,T.C. and Wilcox,W. (1982) Hydrophobic moments and protein structure. Faraday Symp. Chem. Soc., 17, 109-120.
12. Krogh,A., Larsson,B., vonHeijne,G. and Sonnhammer,E.L.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
13. Rost,B., Casadio,R. and Fariselli,P. (1996) Refining neural network predictions for helical transmembrane proteins by dynamic programming. Proc. Int. Conf. Intell. Syst. Mol. Biol., 4, 192-200.
14. vonHeijne,G. (1994) Membrane proteins: From sequence to structure. Annu. Rev. Biophys. Biomol. Struct., 23, 167-192.
15. Eilers,M., Patel,A.B., Liu,W. and Smith,S.O. (2002) Comparison of helix interactions in membrane and soluble α-bundle proteins. Biophys. J., 82, 2720-2736.
16. Traxler,B., Boyd,D. and Beckwith,J. (1993) The topological analysis of integral cytoplasmic membrane proteins. J. Membr. Biol., 132, 1-11.
17. Jayasinghe,S., Hristova,K. and White,S.H. (2001) MPtopo: A database of membrane protein topology. Protein Sci., 10, 455-458.
18. Chen,C.P., Kernytsky,A. and Rost,B. (2002) Transmembrane helix predictions revisited. Protein Sci, 11, 2774-2791.
19. Kall,L., Krogh,A. and Sonnhammer,E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338, 1027-1036.
20. Kernytsky,A. and Rost,B. (2003) Static benchmarking of membrane helix predictions. Nucleic Acids Res., 31, 3642-3644.
21. Godzik,A. (2003) Fold recognition methods. Methods Biochem. Anal., 44, 525-546.
22. Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) Livebench-1: Large-scale automated evaluation of protein structure prediction servers. Protein Sci., 10, 352-361.
23. Marti-Renom,M., Stuart,A., Fiser,A., Sanchez,R., Melo,F. and Šali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
24. Siew,N., Elofsson,A., Rychlewski,L. and Fischer,D. (2000) Maxsub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16, 776-785.
25. Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187-217.
26. Tanaka,S. and Scheraga,H.A. (1976) Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules, 9, 945-950.
27. deArmas,R.R., Diaz,H.G., Molina,R. and Uriarte,E. (2004) Markovian backbone negentropies: Molecular descriptors for protein research. I. Predicting protein stability in arc repressor mutants. Proteins, 56, 715-723.
28. Plaxco,K.W., Simons,K.T. and Baker,D. (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol., 277, 985-994.
29. Grombiha,M.M. and Selvaraj,S. (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction. J. Mol. Biol., 310, 27-32.
30. Barabsi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nature Rev. Genet., 5, 101-113.
31. Ye,Y.Z. and Godzik,A. (2004) Comparative analysis of portein domain organization. Genome Res., 14, 343-353.
32. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.