Comparison of proteins based on segments structural similarity

Acta Biochimica Polonica

Volumn 51, Issue 1, 2004, Pages 161-172

  Plewczynski, Dariusz ^a,b,c   Pas, Jakub ^b   Von Grotthuss, Marcin ^b   Rychlewski, Leszek ^b  

^a UNIVERSITY OF WARSAW   (Poland)

^b BioInfoBank Institute   (Poland)

^c BIOINFOBANK INSTITUTE   (Poland)

Author keywords

3D hit; LiveBench; Protein structure; Protein structure comparison; Structural hashing; ToolShop

Indexed keywords

ACCURACY; ALGORITHM; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MEASUREMENT; PROTEIN DATABASE; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS;

EID: 2342640749     PISSN: 0001527X     EISSN: None     Source Type: Journal    
DOI: 10.18388/abp.2004_3608     Document Type: Review

References (24)

1. Alexandrov NN, Fischer D. (1996) Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. Proteins.; 25: 354-65.
2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. (2000) The Protein Data Bank. Nucleic Acids Res.; 28: 235-42.
3. de Brevern AG, Etchebest C, Hazout S. (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins.; 41: 271-87.
4. Bujnicki JM. (2000) Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol.; 50: 38-44.
5. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. (2001) LiveBench-2: Large-scale automated evaluation of protein structure prediction servers. Proteins.; 45: 184-91.
6. Bystroff C, Baker D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol.; 281: 565-77.
7. Chothia C, Lesk AM. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J.; 5: 823-6.
8. Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. (2001) A study of quality measures for protein threading models. BMC Bioinformatics.; 2: 5.
9. de Filippis V, Sander C, Vriend G. (1994) Predicting local structural changes that result from point mutations. Protein Eng.; 7: 1203-8.
10. Fischer D, Bachar O, Nussinov R, Wolfson H. (1992) An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. J Biomol Struct Dyn.; 9: 769-89.
11. Gibrat JF, Madej T, Bryant SH. (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol.; 6: 377-85.
12. Holm L, Sander C. (1994) The FSSP database of structurally aligned protein fold families. Nucleic Acids Res.; 22: 3600-9.
13. Holm L, Sander C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res.; 26: 316-9.
14. Johnson MS, Sutcliffe MJ, Blundell TL. (1990) Molecular anatomy: Phyletic relationships derived from three-dimensional structures of proteins. J Mol Evol.; 30: 43-59.
15. Levitt M, Gerstein M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A.; 95: 5913-20.
16. Murzin AG. (1994) New Protein Folds. Curr Opin Struct Biol.; 4: 441-9.
17. Murzin AG, Brenner SE, Hubbard T, Chothia C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol.; 247: 536-40.
18. Orengo CA, Jones DT, Thornton JM. (1994) Protein superfamilies and domain super-folds. Nature.; 373: 631-4.
19. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. (1997) CATH - a hierarchic classification of protein domain structures. Structure.; 5: 1093-108.
20. Plewczynski D, Pas J, von Grotthuss M, Rychlewski L. (2002) 3D-Hit: fast structural comparison of proteins. Appl Bioinformatics.; 1: 223-5.
21. Pointing CP, Russel RB. (1995) Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem Sci.; 20: 179-80.
22. Rychlewski L. (2001) ToolShop: prerelease inspections for protein structure prediction servers. Bioinformatics.; 12: 1240-1.
23. Shindyalov IN, Bourne PE. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng.; 11: 739-47.
24. Siew N, Elofsson A, Rychlewski L, Fischer D. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics.; 16: 776-85.