Accelerating protein-protein complex validation by GPU based funnel generation

Michael Zabejansky, Haim J. Wolfson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

A major challenge in protein-protein docking is the distinction between near-native and decoy complex predictions. It has been shown that near native solutions are usually located at the bottom of deep and densely populated funnels in the binding energy plot of the complex. Thus exploration, whether the energy plot of the vicinity of a docking solution is 'funnel like', can serve as a validation of such a solution. Generation of such densely sampled plots, however, is a major computational challenge. We have designed an accurate and highly efficient parallel algorithm for generation of such energy plots and implemented it on a server with 4 GPU processors, each with 2880 cores. The algorithm achieved a speedup of about 150 compared to its serial counterpart, while even outperforming it in the achieved results. While the algorithm proved very useful for near native complex hypothesis validation, it still detects many funnels for decoy solutions, especially those with good shape complementarity.

Original languageEnglish
Title of host publicationProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
EditorsKevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages150-155
Number of pages6
ISBN (Electronic)9781509016105
DOIs
StatePublished - 17 Jan 2017
Event2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China
Duration: 15 Dec 201618 Dec 2016

Publication series

NameProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Conference

Conference2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Country/TerritoryChina
CityShenzhen
Period15/12/1618/12/16

Keywords

  • Binding funnels
  • Docking refinement
  • GPU
  • Protein-protein docking
  • Scoring

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