An efficient algorithm for matching protein binding sites for protein function prediction

Leif Ellingson, Jinfeng Zhang

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

2 Scopus citations

Abstract

Comparing the binding sites of proteins is effective for predicting protein functions based on their structure information. However, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. In this study, we designed a new algorithm based on the iterative closest point (ICP) algorithm. Our algorithm aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of matched superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We show that our method finds more matched atoms than a leading method. For benchmark data, we use the Tanimoto Index as a similarity measure and the nearest neighbor classifier to achieve a classification performance comparable to the best methods in the literature among those that provide both the common atom set and atom correspondences.

Original languageEnglish
Title of host publication2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
Pages289-293
Number of pages5
DOIs
StatePublished - 2011
Event2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011 - Chicago, IL, United States
Duration: Aug 1 2011Aug 3 2011

Publication series

Name2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Conference

Conference2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
CountryUnited States
CityChicago, IL
Period08/1/1108/3/11

Keywords

  • Functional genomics
  • Protein binding site matching
  • Protein function prediction
  • Protein surface matching
  • Structure genomics

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  • Cite this

    Ellingson, L., & Zhang, J. (2011). An efficient algorithm for matching protein binding sites for protein function prediction. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011 (pp. 289-293). (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011). https://doi.org/10.1145/2147805.2147837