Mining residue contacts in proteins using local structure predictions

M. J. Zaki, Shan Jin, C. Bystroff

Research output: Chapter in Book/Report/Conference proceedingConference contribution

18 Citations (Scopus)

Abstract

In this paper, we develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid approach, using a hidden Markov model (HMM) to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy results better than those reported previously.

Original languageEnglish
Title of host publicationProceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages168-175
Number of pages8
ISBN (Print)0769508626, 9780769508627
DOIs
Publication statusPublished - 2000
Externally publishedYes
EventIEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000 - Arlington, United States
Duration: 8 Nov 200010 Nov 2000

Other

OtherIEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000
CountryUnited States
CityArlington
Period8/11/0010/11/00

Fingerprint

Protein folding
Hidden Markov models
Data mining
Amino acids
Nucleation
Association reactions
Proteins

Keywords

  • Amino acids
  • Computational biology
  • Computer science
  • Data mining
  • Databases
  • Hidden Markov models
  • Libraries
  • Peptides
  • Protein engineering
  • Sequences

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Zaki, M. J., Jin, S., & Bystroff, C. (2000). Mining residue contacts in proteins using local structure predictions. In Proceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000 (pp. 168-175). [889604] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2000.889604

Mining residue contacts in proteins using local structure predictions. / Zaki, M. J.; Jin, Shan; Bystroff, C.

Proceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000. Institute of Electrical and Electronics Engineers Inc., 2000. p. 168-175 889604.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Zaki, MJ, Jin, S & Bystroff, C 2000, Mining residue contacts in proteins using local structure predictions. in Proceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000., 889604, Institute of Electrical and Electronics Engineers Inc., pp. 168-175, IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000, Arlington, United States, 8/11/00. https://doi.org/10.1109/BIBE.2000.889604
Zaki MJ, Jin S, Bystroff C. Mining residue contacts in proteins using local structure predictions. In Proceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000. Institute of Electrical and Electronics Engineers Inc. 2000. p. 168-175. 889604 https://doi.org/10.1109/BIBE.2000.889604
Zaki, M. J. ; Jin, Shan ; Bystroff, C. / Mining residue contacts in proteins using local structure predictions. Proceedings - IEEE International Symposium on Bio-Informatics and Biomedical Engineering, BIBE 2000. Institute of Electrical and Electronics Engineers Inc., 2000. pp. 168-175
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