Druggability analysis and prediction based on geometric distances between amino acid residues and protein surface pockets

Makiko Miyoshi, Ayaka Kaneko, Takayuki Itoh, Kei Yura, Masahiro Takatsuka

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

Abstract

Protein is the major component of the organism. A concave (pocket) on a protein surface is known to be thebest target for a drug to react. We previously presented astudy on distance analysis between pockets and amino acidresidue. We firstly identified pockets on the protein surfaceand then calculated distances between atoms of an amino acidresidue and the deepest points or the outer loops of the pockets. We extracted proteins which at least one of the pockets areclose to arbitrary pairs of amino acid residues, calculated theratios of druggable proteins, and visualized the distributionof the ratios as a colored matrix. We suggested from thevisualization results that particular pairs of amino acid residuesmay affect the druggability of the proteins in our previousstudy. This paper presents an extension of our study to explorethe relevance between druggability of proteins and distancesbetween a set of amino acid residues and protein surfacepockets. Our technique treats the pockets as 20-dimensionalvectors consisting of distances to each of amino acid residues, and applies GeodesicSOM with the set of the vectors. Sphericalmaps generated by GeodesicSOM are used to visualizationof distribution of the pockets in the 20-dimensional vectorspace, and estimation of druggability of proteins with the 20-dimensional vectors of the pockets.

Original languageEnglish
Title of host publicationProceedings - NICOGRAPH International 2016, NicoInt 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages21-24
Number of pages4
ISBN (Electronic)9781509023059
DOIs
Publication statusPublished - 2016 Sep 9
Externally publishedYes
Event15th NICOGRAPH International, NicoInt 2016 - Hangzhou, Zhejiang, China
Duration: 2016 Jul 62016 Jul 8

Other

Other15th NICOGRAPH International, NicoInt 2016
CountryChina
CityHangzhou, Zhejiang
Period16/7/616/7/8

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Keywords

  • Druggability
  • Protein
  • Self-Organizing Map
  • Visualization

ASJC Scopus subject areas

  • Signal Processing
  • Media Technology
  • Computer Graphics and Computer-Aided Design

Cite this

Miyoshi, M., Kaneko, A., Itoh, T., Yura, K., & Takatsuka, M. (2016). Druggability analysis and prediction based on geometric distances between amino acid residues and protein surface pockets. In Proceedings - NICOGRAPH International 2016, NicoInt 2016 (pp. 21-24). [7564039] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/NicoInt.2016.4