Cooperative approach for the protein fold recognition

Proteins: Structure, Function and Genetics

Volumn 37, Issue SUPPL. 3, 1999, Pages 126-132

  Ota, Motonori ^a   Kawabata, Takeshi ^a   Kinjo, Akira R ^a,b   Nishikawa, Ken ^a,b  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

CASP; Compatibility function; Homology; Structure prediction; Threading

Indexed keywords

PROTEIN; BACTERIAL PROTEIN; CARRIER PROTEIN; CYANOVIRIN N; CYTOCHROME; LIGASE; RNA 3' TERMINAL PHOSPHATE CYCLASE; RNA 3'-TERMINAL PHOSPHATE CYCLASE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; DATA BASE; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; BACTERIAL PROTEINS; CARRIER PROTEINS; CYTOCHROMES; DATABASES; LIGASES; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0032613334     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(1999)37:3+<126::AID-PROT17>3.0.CO;2-8     Document Type: Article

References (39)

1. Lamer M-R, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current technologies. Proteins 1995;23:337-355.
2. Levitt M. Competitive assessment of protein fold recognition and alignment accuracy. Proteins Suppl 1997;1:92-104.
3. Marchler-Bauer A, Levitt M, Bryant SH. A retrospective analysis of CASP2 threading predictions. Proteins Suppl 1997;1:83-91.
4. Murzin A, Bateman A. Distant homology recognition using structural classification of proteins. Proteins Suppl 1997;1:105-112.
5. Pearson W, Lipman D. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
6. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
7. Altschul SF, Madden TL, Schaffer 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.
8. Thompson J, Higgins D, Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
9. Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res 1999;27:49-54.
10. http://www.ncbi.nlm.nih.gov/PubMed/
11. Ito M, Matsuo Y, Nishikawa K. Prediction of protein secondary structure using the 3D-1D compatibility algorithm. Comput Appl Biosci 1997;13:415-424.
12. Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994;19:55-72.
13. Nishikawa K, Noguchi T. Predicting protein secondary structure based on amino acid sequence. Methods Enzymol 1991;202:31-44.
14. Kawabata T, Doi J. Improvement of protein secondary structure prediction using binary word encoding. Proteins 1997;27:36-46.
15. Hofmann K, Bucher P, Falquet L, Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res 1999;27:215-219.
16. Sussman JL, Lin D, Jianag J, Manning NO, Prilusky J, Ritter O, Abola EE. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Cryst D 1998;54:1078-1084.
17. Matsuo Y, Nishikawa K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 1994;3: 2055-2063.
18. Ota M, Nishikawa K. Feasibility in the inverse protein folding protocol. Protein Sci 1999;8:1001-1009.
19. Matsuo Y, Nishikawa K. Assessment of a protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding, and local conformation. Proteins 1995;23:370-375.
20. Ota M, Kanaya S, Nishikawa K. Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J Mol Biol 1995;248:733-738.
21. Dayhoff MO, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure. 5 suppl. 3, Washington, DC: National Biomedical Research Foundation, 1978. p 345-352.
22. 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.
23. Murzin AG. Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Proteins Suppl 1999;3: 88-103.
24. Raux E, Thermes C, Heathcote P, Rambach A, Warren M. A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis. J Biotechnol 1997;179:3202-3212.
25. Westhead D, Hatton D, Thornton J. An atlas of protein topology cartoons available on the worldwide web. Trends Biochem Sci 1998;23:35-36.
26. Mondragon A, Subbiah S, Almo SC, Drottar M, Harrisori SC. Structure of the amino-terminal domain of phage 434 repressor at 2.0 Å resolution. J Mol Biol 1989;205:189-200.
27. Matsuo Y, Nakamura H, Nishikawa K. Detection of 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions. J Biochem (Tokyo) 1995;118:137-148.
28. 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.
29. Iverson T, Arciero D, Hsu B, Logan M, Hooper A, Rees D. Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea. Nature Struct Biol 1998;5:1005-1012.
30. Gustafson K, Sowder RI, Henderson L, Cardellina JI, McMahon J, Rajamani U, Pannell L, Boyd M. Isolation, primary sequence determination, and disulfide bond structure of cyanovirin-N, an anti-HIV (human immunodeficiency virus) protein from the cyano-bacterium Nostoc ellipsosporum. Biochem Biophys Res Commun 1997;238:223-228.
31. Bewley C, Gustafson KR, Boyd MR, Covell DG, Bax A, Clore GM, Gronenborn AM. Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nature Struct Biol 1998;5:571-578.
32. Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl 1999;3:171-176.
33. Rice D, Fischer D, Weiss R, Eisenberg D. Fold assignments for amino acid sequences of the CASP2 experiment. Proteins Suppl 1997;1:113-122.
34. 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. Mol Cell 1998;2:75-84.
35. McCafferty D, Lessard I, Walsh C. 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.
36. Gallegos M, Michan C, Ramos J. The XylS/AraC family of regulators. Nucleic Acids Res 1993;21:807-810.
37. Fischer D, Eisenberg D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 1997;94:11929-11934.
38. Marchler-Bauer A, Bryant SH. Measures of threading specificity and accuracy. Proteins Suppl 1997;1:74-82.
39. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.