An efficient mechanism for prediction of protein-ligand interactions based on analysis of protein tertiary substructures

Tien-Hao Chang, Chien Yu Chen, Yen Jen Oyang, Hsueh Fen Juan, Hsuan Cheng Huang

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

4 Citations (Scopus)

Abstract

Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, an efficient mechanism for identifying possible protein-ligand interactions based on analysis of protein tertiary substructures is proposed. In one experiment reported in this papert, the proposed prediction mechanism has been exploited to obtain some clues about a hypothesis that the biochemists have been speculating. The main distinction in the design of the prediction mechanism is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in a cave of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the α-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a 3-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.11 to 9.79 times.

Original languageEnglish
Title of host publicationProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
Pages427-433
Number of pages7
DOIs
Publication statusPublished - 2004 Sep 24
EventProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 - Taichung, Taiwan
Duration: 2004 May 192004 May 21

Publication series

NameProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Other

OtherProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
CountryTaiwan
CityTaichung
Period04-05-1904-05-21

All Science Journal Classification (ASJC) codes

  • Engineering(all)

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    Chang, T-H., Chen, C. Y., Oyang, Y. J., Juan, H. F., & Huang, H. C. (2004). An efficient mechanism for prediction of protein-ligand interactions based on analysis of protein tertiary substructures. In Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 (pp. 427-433). (Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004). https://doi.org/10.1080/00472330480000201