TM-align: A protein structure alignment algorithm based on the TM-score

Nucleic Acids Research

Volumn 33, Issue 7, 2005, Pages 2302-2309

  Zhang, Yang ^a   Skolnick, Jeffrey ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION FUNCTION; INTERMETHOD COMPARISON; INTERNET; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FOLDING; PROTEIN STRUCTURE; ROTATION; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; COMPARATIVE STUDY; EVALUATION; MOLECULAR GENETICS; PROTEIN DATABASE; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 17644392830     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki524     Document Type: Article

References (40)

1. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
2. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
3. Moult,J., Fidelis,K., Zemla,A. and Hubbard,T. (2003) Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins, 53, 334-339.
4. Skolnick,J., Fetrow,J.S. and Kolinski,A. (2000) Structural genomics and its importance for gene function analysis. Nat. Biotechnol., 18, 283-287.
5. Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
6. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
7. Chance,M.R., Fiser,A., Sali,A., Pieper,U., Eswar,N., Xu,G., Fajardo,J.E., Radhakannan,T. and Marinkovic,N. (2004) High-throughput computational and experimental techniques in structural genomics. Genome Res., 14, 2145-2154.
8. Zhang,Y. and Skolnick,J. (2004) Automated structure prediction of weakly homologous proteins on a genomic scale. Proc. Natl Acad. Sci. USA, 101, 7594-7599.
9. Kihara,D., Zhang,Y., Lu,H., Kolinski,A. and Skolnick,J. (2002) Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalim genome. Proc. Natl Acad. Sci. USA, 99, 5993-5998.
10. Arakaki,A.K., Zhang,Y. and Skolnick,J. (2004) Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics, 20, 1087-1096.
11. Kabsch,W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 34, 827-828.
12. Betancourt,M.R. and Skolnick,J. (2001) Universal similarity measure for comparing protein structures. Biopolymers, 59, 305-309.
13. Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
14. Levitt,M. and Gerstein,M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc. Natl Acad. Sci. USA, 95, 5913-5920.
15. Lathrop,R.H. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7, 1059-1068.
16. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
17. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
18. Kihara,D. and Skolnick,J. (2003) The PDB is a covering set of small protein structures. J. Mol. Biol., 334, 793-802.
19. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
20. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
21. Hubbard,T.J. (1999) RMS/coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions. Proteins, 37, (Suppl. 3), 15-21.
22. Kolodny,R., Koehl,P. and Levitt,M. (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol., 346, 1173-1188.
23. Leplae,R. and Hubbard,T.J. (2002) MaxBench: Evaluation of sequence and structure comparison methods. Bioinformatics, 18, 494-495.
24. Sierk,M.L. and Pearson,W.R. (2004) Sensitivity and selectivity in protein structure comparison. Protein Sci., 13, 773-785.
25. Novotny,M., Madsen,D. and Kleywegt,G.J. (2004) Evaluation of protein fold comparison servers. Proteins, 54, 260-270.
26. Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol., 301, 665-678.
27. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
28. Aloy,P., Stark,A., Hadley,C. and Russell,R.B. (2003) Predictions without templates: New folds, secondary structure, and contacts in CASP5. Proteins, 53, 436-456.
29. Zhang,Y. and Skolnick,J. (2005) The protein structure prediction problem could be solved using the current PDB library. Proc. Natl Acad. Sci. USA, 102, 1029-1034.
30. Skolnick,J., Kihara,D. and Zhang,Y. (2004) The protein structure prediction problem could be solved using the current PDB library. Proteins, 56, 502-518.
31. Zhang,Y. and Skolnick,J. (2004) SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem., 25, 865-871.
32. Murray,A.J., Head,J.G., Barker,J.J. and Brady,R.L. (1998) Engineering an intertwined form of CD2 for stability and assembly. Nature Struct. Biol., 5, 778-782.
33. + channels controls assembly with apo-calmodulin. J. Biol. Chem., 277, 4558-4564.
34. Zhang,Y., Kolinski,A. and Skolnick,J. (2003) TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys. J., 85, 1145-1164.
35. Levinthal,C. (1969) How to fold graciously. In Debrunner,P., Tsibris,J. and Munck,E. (eds), Mossbauer Spectroscopy in Biological Systems. University of Illinois Press, Illinois, pp. 22-24.
36. Zhang,Y. and Skolnick,J. (2004) Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys. J., 87, 2647-2655.
37. Bradley,P., Chivian,D., Meiler,J., Misura,K.M., Rohl,C.A., Schief,W.R., Wedemeyer,W.J., Schueler-Furman,O., Murphy,P., Schonbrun,J. et al. (2003) Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation. Proteins, 53, 457-468.
38. Holm,L. and Sander,C. (1995) Dali: A network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
39. Jones,E.Y., Davis,S.J., Williams,A.F., Harlos,K. and Stuart,D.I. (1992) Crystal structure at 2.8 Å resolution of a soluble form of the cell adhesion molecule CD2. Nature, 360, 232-239.
40. 2+/calmodulin. Nature, 410, 1120-1124.