Library of local descriptors models the core of proteins accurately

Proteins: Structure, Function and Genetics

Volumn 69, Issue 3, 2007, Pages 499-510

  Drabikowski, Michał ^a   Nowakowski, Szymon ^a   Tiuryn, Jerzy ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

Local descriptor of protein structure; Local structure; Predicting sequence from structure; Protein representation

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; FEASIBILITY STUDY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN STRUCTURE; REPRODUCIBILITY;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACIDS; DATABASES, PROTEIN; FEASIBILITY STUDIES; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT;

EID: 35448944862     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21393     Document Type: Article

References (22)

1. Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins: Struct Funct Genet 2003;53:436-456.
2. Unger R, Harel D, Wherland S, Sussman JL. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins: Struct Funct Genet 1989;5:355-373.
3. Micheletti C, Seno F, Maritan A. Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins: Struct Funct Genet 2000;41:271-287.
4. Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol 2002;323:297-307.
5. Bradley J, Tsai J. Some fundamental aspects of building protein structures from fragment libraries. Proti Sci 2004;12:1636-1650.
6. Yang A, Wang L. Local structure prediction with local structure-based sequence profiles. Bioinformatics 2003;19:1267-1274.
7. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281: 565-577.
8. Etchebest C, Benros C, Hazout S, Brevem AG. A structural alphabet for local protein structures: improved prediction method. Proteins: Struct Funct Genet 2005;59:810-827.
9. 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;268:209-225.
10. Hvidsten TR, Kryshtafovych A, Komorowski J, Fidelis K. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics 2003;19:II81-II91.
11. Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000; 28:254-256.
12. Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis. Cambridge: Cambridge University Press 1998.
13. Altschul SF. Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 1991;219:555-565.
14. Smith RF, Smith TF. Automatic generation of primary sequence patterns from sets of related protein sequences. PNAS 1990;87:118-122.
15. Tatusov RL, Altschul SF, Koonin EV. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. PNAS 1994;91:12091-12095.
16. Sjolander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appli Biosci 1996;12:327-345.
17. Garey MR, Johnson DS. Computers and intractability. A guide to the theory of NP-completeness. New York: W. H. Freedman and Company 2000.
18. Nowakowski S, Tiuryn J. A new approach to the assessment of the quality of predictions of transcription factor binding sites. J Biomed Informat 2007;40:139-149.
19. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol 1986;188:415-431.
20. Kullback S, Leibler RA. On information and sufficiency. Ann Math Stat 1951;22(1):79-86.
21. Altschul SF, Madden TL, Schffer 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.
22. Abagyan RA, Batalov S. Do aligned sequences share the same fold? J Mol Biol 1997;273:355-368.