Acceleration of a protein structure comparison algorithm on FPGA

Arpad Goretity, Zoltan Nagy, Z. Gáspári

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

Abstract

Proteins are among the most fundamental molecules in living organisms. Investigation and comparison of their three-dimensional structure is an important task in structural bioinformatics as global and local similarities can be of functional importance. Structure alignment and comparison is computationally intensive, so typically a number of simplifications are used for practical reasons. However, these can not always be justified on a biological or biochemical basis, and might lead to unreliable results. In this paper we describe the development and application of a method based on local structural information, suitable for comprehensive analysis of the more than 100,000 structures available today. The approach is implemented on an FPGA board allowing reasonable runtime and thus offering the possibility of parameter tuning on very large, unbiased datasets.

Original languageEnglish
Title of host publication2017 European Conference on Circuit Theory and Design, ECCTD 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781538639740
DOIs
Publication statusPublished - Oct 31 2017
Event2017 European Conference on Circuit Theory and Design, ECCTD 2017 - Catania, Italy
Duration: Sep 4 2017Sep 6 2017

Other

Other2017 European Conference on Circuit Theory and Design, ECCTD 2017
CountryItaly
CityCatania
Period9/4/179/6/17

ASJC Scopus subject areas

  • Hardware and Architecture
  • Electrical and Electronic Engineering
  • Electronic, Optical and Magnetic Materials

Fingerprint Dive into the research topics of 'Acceleration of a protein structure comparison algorithm on FPGA'. Together they form a unique fingerprint.

  • Cite this

    Goretity, A., Nagy, Z., & Gáspári, Z. (2017). Acceleration of a protein structure comparison algorithm on FPGA. In 2017 European Conference on Circuit Theory and Design, ECCTD 2017 [8093342] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ECCTD.2017.8093342