Structure classification-based assessment of CASP3 predictions for the fold recognition targets

Proteins: Structure, Function and Genetics

Volumn 37, Issue SUPPL. 3, 1999, Pages 88-103

  Murzin, Alexey G ^a  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

Author keywords

Distant homology; Structure comparison; Structure prediction; Threading

Indexed keywords

ANALYTIC METHOD; ARTICLE; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ESCHERICHIA COLI; HUMAN; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY;

BACTERIAL PROTEIN; FLAVODOXIN; FUNGAL PROTEIN; PROTEIN;

BACTERIAL PROTEINS; ESCHERICHIA COLI; FLAVODOXIN; FUNGAL PROTEINS; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0032605908     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(1999)37:3+<88::aid-prot13>3.0.co;2-3     Document Type: Article

References (43)

1. Prodromou C, Roe SM, O'Brien R, Ladbury JE, Piper PW, Pearl LH. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell 1997;90: 65-75.
2. Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 1991;351:624-629.
3. Zemla A, Venclovas Č, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins Suppl 1999; 3:22-29. The CASP archives are available at URL http:// PredictionCenter.llnl.gov/
4. Hubbard TJP. RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Proteins Suppl 1999;3:15-21.
5. Lackner P, Koppensteiner WA, Dominigues FS, Sippl MJ. Automated large scale evaluation of protein structure predictions. Proteins Suppl 1999;3:7-14.
6. Feng Z-K, Sippl MJ. Optimum superposition of protein structures, ambiguities and implications. Folding & Design 1996;1:123-132.
7. 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.
8. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
9. Gibrat J-F, Madej T, Bryant SH. Surprising similarities in structure comparison. Current Opinion Struct Biol 1996;6:377-385. The VAST results of the target structure comparisons are available at URL http://www.ncbi.nlm.nih.gov/Structure/casp3/ casp3vast.html
10. Saadat D, Harrison DHT. The crystal structure of methylglyoxal synthase from Esherichia coli. Structure 1999;7:309-317.
11. Thoden BJ, Holden HM, Wesenberg G, Raushel FM, Rayment I. Structure of carbamoyl phosphate synthase: a journey of 96 Å from substrate to product. Biochemistry 1997;36:6305-6313.
12. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
13. Skarzynski T, Mistry A, Wonacott A, Hutchinson SE, Kelly VA, Duncan K. Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin. Structure 1996;4:1465-1474.
14. Iverson TM, Arciero DM, Hsu BT, Logan MSP, Hooper AB, Rees DC. Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea. Nature Struct Biol 1998;5:1005-1012.
15. Igarashi N, Moriyama H, Fujiwara T, Fukumori Y, Tanaka N. The 2.8 Å structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. Nature Struct Biol 1997;4:276-284.
16. Beamer LJ, Pabo CO. Refined 1.8 Å crystal structure of the lambda represser-operator complex. J Mol Biol 1992;227:177-196.
17. Bussiere DE, Pratt SD, Katz L, Severin JM, Holzman T, Park CH. The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Molecular Cell 1998;2:75-84.
18. McCafferty DG, Lessard IA, Walsh CT. Mutational analysis of potential zinc-binding residues in the active site of the enterococcal D-Ala-D-Ala dipeptidase VanX. Biochemistry 1997;36:10498-10505.
19. Al-Karadaghi S, Hansson M, Nikonov S, Jonsson B, Hederstedt L. Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Structure 5:1501-1510.
20. Reitzer R, Gruber K, Jogl G, Wagner UG, Bothe H, Buckel W, Kratky C. Structure of the coenzyme B12 dependent enzyme glutamate mutase from Clostridium cochlearium. Structure 1999; 7:891-902.
21. 12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 Å resolution. Structure 1996;4:339-350.
22. Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC. Structure of translation initiation factor 5a from Pyrobaculum aerophilum at 1.75 Å resolution. Structure 1998;6:1207-1214.
23. Kim KK, Hung LW, Yokota H, Kim R, Kim SH. Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution. Proc Natl Acad Sci U S A. 1998;95:10419-10424.
24. Hung LW, Kim KK, Yokota H, Kim R, Kim SH. The crystal structures of a homologue of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 resolution. Abstract W0155 of the ACA1998 annual meeting, http://www.hwi.buffalo.edu/ACA/ACA98/abstracts/
25. Rhee S, Martin RG, Rosner JL, Davies DR. A novel DNA-binding motif in MarA: The first structure for an AraC family transcriptional activator. PNAS, 95:10413-10418.
26. Ogata K, Morikawa S, Nakamura H, et al. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell 1994;79:639-648.
27. Lau AY, Schaerer OD, Samson L, Verdine GL, Ellenberger T. Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell 1998;95:249-258.
28. Met. EMBO J 1998;17:6819-6826.
29. Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL. Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure 1996;4:253-264.
30. Benning MM, Wesenberg G, Liu R, Taylor KL, Dunaway-Mariano D, Holden HM. The three-dimensional structure of 4-hydroxybenzoyl-CoA thioestease from Pseudomonas sp. Strain CBS-3. J Biol Chem 1988;273:33572-33579.
31. Owen DJ, Vallis Y, Noble MEM, et al. A structural explanation for the binding of multiple ligands by the α-adaptin appendage domain. Cell 1999;97:805-815, 1999.
32. Banfield MJ, Barker JJ, Perry ACF, Brady LR. Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction. Structure 1998;6:1245-1254.
33. Xiao B, Shi G, Chen X, Yan H, Ji X. Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents. Structure 1999;7:489-496.
34. Ermler U, Merckel M, Thauer R, Shima S. Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability. Structure 1997;5:635-646.
35. Cambach K, Walke S, Young R, et al. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 1999;96:375-387.
36. Hohenester E, Sasaki T, Timpl R.: Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily. Nature Struct Biol 1999;6:228-232.
37. Resnik D, Pearson A, Krigier M. The SRCR superfamily: a family reminiscent of the Ig superfamily. Trends Biochem Sci 1994;19: 5-8.
38. Lowe J, Amos LA. Crystal structure of the bacterial cell-division protein FtsZ. Nature 391:203-206.
39. Yang F, Gustafson KR, Boyd MR, Wlodawer A. Crystal structure of Escherichia coli HdeA. Nature Struct Biol 1998;5:763-764.
40. Slupsky CM, Gentile LN, Donaldson LW, et al. Structure of the Ets-1 pointed domain and mitogen-activated protein kinase phosphorylation site. Proc Natl Acad Sci U S A 1998;95:12129-12134.
41. Thanos CD, Goodwill KE, Bowie JU. Oligomeric structure of the human EphB2 receptor SAM domain. Science 1999;283:833-836.
42. Bewley CA, Gustafson KR, Boyd MR, Covell DG, Bax A, Clore GM. Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nature Struct Biol 1998;5:571-578.
43. Weigelt J, Brown SE, Milles CS, Dixon NE, Otting G. NMR structure of the N-terminal domain of E. coli DnaB helicase: implications for structure rearrangements in the helicase hexamer and its biological function. Structure 1999;7:691-698.