Home LiteratureArticle Details
PMID: 11717394 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Protein threading by learning.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 98 ·No. 25 ·2001-12-04 ·Pages 14350-5

Chang I, Cieplak M, Dima RI, Maritan A, Banavar JR

Abstract

By using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins. These parameters provide a quantitative measure of the propensities of amino acids to be buried or exposed and to be in a given secondary structure and are a good starting point for solving both the threading and design problems.

MeSH Terms
Amino Acid Sequence Drug Design Models, Chemical Models, Statistical Molecular Sequence Data Protein Folding Protein Structure, Secondary Proteins/chemistry
Chemicals
Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Chang I
Department of Physics, 104 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
Cieplak M
Dima R I
Maritan A
Banavar J R
References (30)
30 references, click to expand
  1. The Protein Data Bank.
    Nucleic Acids Res. 2000 Jan 1;28(1):235-42 PMID: 10592235
  2. Statistical mechanics of protein-like heteropolymers.
    Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4904-7 PMID: 10220391
  3. On the design and analysis of protein folding potentials.
    Proteins. 2000 Jul 1;40(1):71-85 PMID: 10813832
  4. Two exposed amino acid residues confer thermostability on a cold shock protein.
    Nat Struct Biol. 2000 May;7(5):380-3 PMID: 10802734
  5. Toward protein tertiary structure recognition by means of associative memory hamiltonians.
    Science. 1989 Oct 20;246(4928):371-3 PMID: 17747919
  6. Contact potential that recognizes the correct folding of globular proteins.
    J Mol Biol. 1992 Oct 5;227(3):876-88 PMID: 1404392
  7. Conformation of polypeptides and proteins.
    Adv Protein Chem. 1968;23:283-438 PMID: 4882249
  8. A surprising simplicity to protein folding.
    Nature. 2000 May 4;405(6782):39-42 PMID: 10811210
  9. From Levinthal to pathways to funnels.
    Nat Struct Biol. 1997 Jan;4(1):10-9 PMID: 8989315
  10. Principles that govern the folding of protein chains.
    Science. 1973 Jul 20;181(4096):223-30 PMID: 4124164
  11. Dominant forces in protein folding.
    Biochemistry. 1990 Aug 7;29(31):7133-55 PMID: 2207096
  12. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.
    Macromolecules. 1976 Nov-Dec;9(6):945-50 PMID: 1004017
  13. Protein tertiary structure recognition using optimized Hamiltonians with local interactions.
    Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9029-33 PMID: 1409599
  14. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.
    Proteins. 2000 Nov 1;41(2):192-201 PMID: 10966572
  15. How to derive a protein folding potential? A new approach to an old problem.
    J Mol Biol. 1996 Dec 20;264(5):1164-79 PMID: 9000638
  16. Some factors in the interpretation of protein denaturation.
    Adv Protein Chem. 1959;14:1-63 PMID: 14404936
  17. Proteins. One thousand families for the molecular biologist.
    Nature. 1992 Jun 18;357(6379):543-4 PMID: 1608464
  18. Measures of residue density in protein structures.
    Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12494-9 PMID: 10535950
  19. A new approach to protein fold recognition.
    Nature. 1992 Jul 2;358(6381):86-9 PMID: 1614539
  20. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment.
    Protein Sci. 1996 Jun;5(6):1043-59 PMID: 8762136
  21. SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    J Mol Biol. 1995 Apr 7;247(4):536-40 PMID: 7723011
  22. Environment-dependent residue contact energies for proteins.
    Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2550-5 PMID: 10706611
  23. Enlarged representative set of protein structures.
    Protein Sci. 1994 Mar;3(3):522-4 PMID: 8019422
  24. New algorithm for protein design.
    Phys Rev Lett. 1996 Jan 8;76(2):323-326 PMID: 10061072
  25. A method to identify protein sequences that fold into a known three-dimensional structure.
    Science. 1991 Jul 12;253(5016):164-70 PMID: 1853201
  26. Optimal Protein Design Procedure.
    Phys Rev Lett. 1996 Aug 26;77(9):1901-1904 PMID: 10063200
  27. Distance-dependent, pair potential for protein folding: results from linear optimization.
    Proteins. 2000 Oct 1;41(1):40-6 PMID: 10944392
  28. Navigating the folding routes.
    Science. 1995 Mar 17;267(5204):1619-20 PMID: 7886447
  29. Scoring functions in protein folding and design.
    Protein Sci. 2000 Apr;9(4):812-9 PMID: 10794424
  30. Protein design by binary patterning of polar and nonpolar amino acids.
    Science. 1993 Dec 10;262(5140):1680-5 PMID: 8259512
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.241133698
Published
2001-12-04
Epub
2001-00-20
Pages
14350-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC64685
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.241133698 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2