Evaluation of Protein Fold Comparison Servers

Proteins: Structure, Function and Genetics

Volumn 54, Issue 2, 2004, Pages 260-270

  Novotny, Marian ^a   Madsen, Dennis ^b   Kleywegt, Gerard J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b NOVO NORDISK A S   (Denmark)

Author keywords

Fold classification; Protein fold; Protein structure; Structural bioinformatics; Structure comparison; Structure superposition

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPARATIVE STUDY; COMPUTER SIMULATION; DATA BASE; EVALUATION; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; CYCLOPHILINS; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; USER-COMPUTER INTERFACE;

EID: 0347719528     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10553     Document Type: Article

References (46)

1. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
3. Holm L, Sander C. Searching protein structure databases has come of age. Proteins 1994;19:165-173.
4. Brown NP, Orengo CA, Taylor WR. A protein structure comparison methodology. Comput Chem 1996;20:359-380.
5. Eidhammer I, Jonassen I, Taylor WR. Structure comparison and structure patterns. J Comput Biol 2000;7:685-716.
6. Koehl P. Protein structure similarities. Curr Opin Struct Biol 2001;11:348-353.
7. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6:377-385.
8. Kleywegt GJ, Jones TA. Detecting folding motifs and similarities in protein structures. Methods Enzymol 1997;277:525-545.
9. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
10. Jung J, Lee B. Protein structure alignment using environmental profiles. Protein Eng 2000;13:535-543.
11. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
12. Madsen D, Kleywegt GJ. Interactive motif and fold recognition in protein structures. J Appl Crystallogr 2002;35:137-139.
13. Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci USA 1998;95:5913-5920.
14. Singh AP, Brutlag DL. Hierarchical protein structure superposition using both secondary structure and atomic representations. Proc Intell Syst Mol Biol 1997;97:284-293.
15. Horn BKP. Closed form solution ofabsolute orientation using unit quaternions. J Opt Soc Am 1987;4:629-642.
16. Kawabata T, Nishikawa K. Protein structure comparison using the Markov transition model of evolution. Proteins 2000;41:108-122.
17. Carugo O, Pongor S. Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison. J Mol Biol 2002;315:887-898.
18. Vlahovicek K, Carugo O, Pongor S. The PRIDE server for protein three-dimensional similarity. J Appl Crystallogr 2002;35:648-649.
19. Lu G. TOP: a new method for protein structure comparisons and similarity searches. J Appl Crystallogr 2000;33:176-183.
20. Gilbert D, Westhead D, Nagano N, Thornton J. Motif-based searching in TOPS protein topology databases. Bioinformatics 1999;15:317-326.
21. Westhead DR, Hatton DC, Thornton JM. An atlas of protein topology cartoons available on the World-Wide Web. Trends Biochem Sci 1998;23:35-36.
22. Martin ACR. The ups and downs of protein topology; rapid comparison of protein structure. Protein Eng 2000;13:829-837.
23. Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol 1996;266:617-635.
24. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995;23:356-369.
25. Harrison A, Pearl F, Mott R, Thornton J, Orengo C. Quantifying the similarities within fold space. J Mol Biol 2002;323:909-926.
26. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
27. Brenner SE, Chothia C, Hubbard TJ, Murzin AG. Understanding protein structure: using scop for fold interpretation. Methods Enzymol 1996;266:635-643.
28. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
29. Holm L, Sander C. The FSSP database of structurally aligned protein fold families. Nucleic Acids Res 1994;22:3600-3609.
30. Holm L, Sander C. Mapping the protein universe. Science 1996;273:595-602.
31. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
32. Hadley C, Jones DT. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure 1999;7:1099-1112.
33. McGuffin LJ, Bryson K, Jones DT. What are the baselines for protein fold recognition? Bioinformatics 2001;17:63-72.
34. Fischer D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means ofa comprehensive benchmark. Proc Pacific Symp Biocomput 1996;96:300-318.
35. Groft CM, Beckmann R, Sali A, Burley SK. Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol 2000;7:1156-1164.
36. Paoli M. An elusive propeller-like fold. Nat Struct Biol 2001;9:744.
37. Groft CM, Beckmann R, Sali A, Burley SK. Response to Paoli. Nat Struct Biol 2001;9:745.
38. Kleywegt GJ. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr 1996;D52:842-857.
39. van Aalten DMF, Milne KG, Zou JY, Kleywegt GJ, Bergfors T, Ferguson MAJ, Knudsen J, Jones TA. Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein. J Mol Biol 2001;309:181-192.
40. Murray-Rust J, Leiper J, McAlister M, Phelan J, Tilley S, Santa Maria J, Vallance P, McDonald N. Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimethylarginine dimethylaminohydrolase. Nat Struct Biol 2001;8:679-683.
41. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
42. Holm L, Sander C. Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol 1996;266:653-662.
43. Kleywegt GJ, Jones TA. Halloween...masks and bones. In: Bailey S, Hubbard R, Waller DA, editors. From first map to final model. Daresbury: SERC Daresbury Laboratory; 1994. p 59-66.
44. Gilbert D, Westhead D, Viksna J, Thornton J. A computer system to perform structure comparison using TOPS representations of protein structure. Comput Chem 2001;26:23-30.
45. Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA. Assigning genomic sequences to CATH. Nucleic Acids Res 2000;28:278-282.
46. Subbiah S, Laurents DV, Levitt M. Structural similarity of DNA binding domains of bacteriophage repressors and the globin core. Curr Biol 1993;3:141-148.