A method for the improvement of threading-based protein models

Proteins: Structure, Function and Genetics

Volumn 37, Issue 4, 1999, Pages 592-610

  Kolinski, Andrzej ^a,b   Rotkiewicz, Piotr ^a,b   Ilkowski, Bartosz ^a,b   Skolnick, Jeffrey ^a  

^a DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Homology modeling; Lattice protein models; Monte Carlo simulations; Protein modeling; Protein structure prediction; Threading

Indexed keywords

PROTEIN;

ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; SYSTEM ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; EVALUATION STUDIES; METHODS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE DESIGN;

EID: 0032706408     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<592::AID-PROT10>3.0.CO;2-2     Document Type: Article

References (28)

1. Bowie JU, Luethy R, Eisenberg D. A method to identify protein sequences that fold into a known three dimensional structure. Science 1991;253:164-170.
2. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
3. Godzik A, Skolnick J, Kolinski A. A topology fingerprint approach to the inverse folding problem. J Mol Biol 1992;227:227-238.
4. Miller RT, Jones DT, Thornton JM. Protein fold recognition by sequence threading tools and assessment techniques. FASEB 1996;10:171-178.
5. Zhang B, Jaroszewski L, Rychlewski L, Godzik A. Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des 1997;2:307-317.
6. Hu W-P, Godzik A, Skolnick J. On the origin of sequence-structure specificity. How does an inverse folding approach work? Protein Eng 1997;10:317-331.
7. Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through folding motif. Proteins 1993; 16:92-112.
8. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995;23:356-369.
9. 1ribonucleases. J Mol Biol 1998;281:949-968.
10. Fetrow J, Godzik A, Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-structure-function paradigm: identification of proteins exhibiting the glutaredoxin/ thioredoxin disulfide oxireductase activity. J Mol Biol 1998;282: 703-711.
11. Sali A, Overington JP, Johnson MS, Blundell TL. From comparison of protein sequences and structures to protein modeling and design. TIBS 1990;15:235-250.
12. Aszodi A, Tylor WR. Homology modeling by distance geometry. Fold Des 1996;1:325-334.
13. Jaroszewski L, Pawlowski K, Godzik A. Multiple model approach: exploring the limits of comparative modeling. J Mol Modelling 1998;4:294-309.
14. Jaroszewski L, Rychlewski L, Zhang B, Godzik A. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 1998;7:1431-1440.
15. Wodak SJ, Rooman MJ. Generating and testing protein folds. Curr Opin Struct Biol 1993;3:247-259.
16. Kolinski A, Jaroszewski L, Rotkiewicz P, Skolnick J. An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side groups centers of mass. J Phys Chem 1998;102:4628-4637.
17. Kolinski A, Skolnick J. Assembly of protein structure from sparse experimental data. An efficient Monte Carlo model. Proteins 1998;32:475-494.
18. Kolinski A, Skolnick J. Lattice models of protein folding, dynamics and thermodynamics. Austin, TX: RG Landes; 1996. 200 p.
19. Skolnick J, Kolinski A, Ortiz AR. MONSSTER: A method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241.
20. Bernstein FC, Koetzle TF, Williams GJB, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
21. Binder K. The Monte Carlo method in condensed matter physics: Institut Für Physik, Johannes Gutenberg-Universität, Mainz, 1991.
22. Godzik A, Skolnick J, Kolinski A. Regularities in interaction patterns of globular proteins. Protein Eng 1993;6:801-810.
23. Milik M, Kolinski A, Skolnick J. Neural network system for the evaluation of side chain packing in protein structures. Protein Eng 1995;8:225-236.
24. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
25. Koradi R. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
26. Altschul SF, Madden TL, Schaefer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997;25:3389-3402.
27. Hobohom U, Scharf M, Schneider R, Sander C. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci 1992;1:409-417.
28. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.