Protein local structure prediction from sequence

Proteins: Structure, Function and Genetics

Volumn 50, Issue 4, 2003, Pages 572-579

  Hunter, Cornelius G ^a   Subramaniam, Shankar ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Fragment clustering; Local structure; Protein fragments; Protein structure; Structure prediction

Indexed keywords

BASIC FIBROBLAST GROWTH FACTOR; CALCIUM BINDING PROTEIN; CARRIER PROTEIN; ERYTHRINA EXTRACT; FERREDOXIN; GLOBULAR PROTEIN; GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR; INTERLEUKIN 4; MYELIN; NUCLEOSIDE DIPHOSPHATE KINASE; RIBOSOME PROTEIN; RUBREDOXIN; TETANUS TOXIN; TRYPSIN INHIBITOR;

AMINO ACID SEQUENCE; ARTICLE; HYDROPHOBICITY; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE;

ANIMALS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN;

EID: 0037342404     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10310     Document Type: Article

References (34)

1. Creighton TE. Proteins: structures and molecular properties, 2nd ed. New York W.H. Freeman; 1993.
2. Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988;202:865-884.
3. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
4. Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997;27:329-335.
5. Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol 1977;114:181-239.
6. Ramakrishnan C, Soman KV. Identification of secondary structures in globular proteins - a new algorithm. Int J Peptide Protein Res 1982;20:218-237.
7. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
8. Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 1988;3:71-84.
9. Sklenar H, Etchebest C, Lavery R. Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989;6:46-60.
10. Petersen TN, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert GP, Lund O. Prediction of protein secondary structure at 80% accuracy. Proteins 2000;41:17-20.
11. Unger R, Sussman JL. The importance of short structural motifs in protein structure analysis. Comp Aided Mol Des 1993;7:457-472.
12. Jones DT, Thirup S. Using known substructures in protein model building and crystallography. EMBO J 1986;5:819-822.
13. Claessens M, Van Cutsem E, Lasters I, Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng 1989;2:335-345.
14. Pappas GJ. Protein three-dimensional structure: theoretical and computational aspects of structure prediction based on the amino acid sequence. University of Illinois PhD Thesis, Urbana, 1999.
15. Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure mofits in proteins. J Mol Biol 1990;213: 327-336.
16. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507-533.
17. Fidelis K, Stern PS, Bacon D, Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994;7:953-960.
18. Hunter CG, Subramaniam S. Protein fragment clustering and canonical local shapes. Proteins 2003;50:580-588.
19. Gruebele M, Sabelko J, Ballew R, Ervin J. Laser temperature jump induced protein refolding. Acc Chem Res 1998;31:699-707.
20. Ramachandra Shastry MC, Sauder JM, Roder H. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Acc Chem Res 1998;31:717-725.
21. Dyer RB, Gai F, Woodruff WH, Gilmanshin R, Callender RH. Infrared studies of fast events in protein folding. Acc Chem Res 1998;31:709-716.
22. Eaton WA, Munoz V, Thompson PA, Henry ER, Hofrichter J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc Chem Res 1998;31:745-753.
23. Breipohl, AM. Probabilistic systems analysis. New York: John Wiley & Sons; 1970.
24. Shepherd AJ, Gorse D, Thornton JM. Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 1999;5:1045-1055.
25. Pal L, Basu G. Neural network prediction of 3(10)-helices in proteins. Indian J Biochem Biophys 2001;38:107-114.
26. Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R. Clustering protein sequences-structure prediction by transitive homology. Bioinformatics 2001;10:935-941.
27. Simons KT, Strauss C, Baker D. Prospects for ab initio protein structural genomics. J Mol Biol 2000;306:1191-1199.
28. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281:565-577.
29. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions. J Mol Biol 1997;267:209-225.
30. Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins 1997;Suppl 1:167-171.
31. Han KF, Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci USA 1996;93:5814-5818.
32. Han KF, Baker D. Recurring local sequence motifs in proteins. J Mol Biol 1995;251:176-187.
33. Capaldi A, Radford S. Kinetic studies of beta-sheet protein folding. Curr Opin Struct Biol 1998;8:86-92.
34. Nishimura C, Prytulla S, Jane DH, Wright PE. Conservation of folding pathways in evolutionary distant globin sequences. Nat Struct Biol 2000;7:679-686.