New algorithm and web server for finding proteins with similar 3D structures

Zaixin Lu, Zhiyu Zhao, Sergio Garcia, Bin Fu

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

2 Scopus citations

Abstract

We develop a new algorithm for finding similar protein structures in the protein databank. It can return a set of protein structures that are similar to the given protein structure in two minutes. In order to compare the performance with other webservers, we develop a a symmetric difference model between the two sets of protein structures which are outputted by two different softwares when the same protein structure is given as input. It is compared with the similar tool of Secondary Structure Matching (SSM) at address "http://www.ebi.ac. uk/msd-srv/ssm/" and shows competitive performance. Our algorithm has been implemented as a web-server at address "http://fpsa.cs.panam.edu/" supported by a cluster of computers for public access.

Original languageEnglish (US)
Title of host publicationProceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
Pages674-680
Number of pages7
StatePublished - Dec 1 2008
Event2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008 - Las Vegas, NV, United States
Duration: Jul 14 2008Jul 17 2008

Publication series

NameProceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008

Other

Other2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
CountryUnited States
CityLas Vegas, NV
Period7/14/087/17/08

Keywords

  • Alignment
  • And searching
  • Protein 3D structures

ASJC Scopus subject areas

  • Computer Science Applications
  • Software
  • Biomedical Engineering
  • Health Informatics

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  • Cite this

    Lu, Z., Zhao, Z., Garcia, S., & Fu, B. (2008). New algorithm and web server for finding proteins with similar 3D structures. In Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008 (pp. 674-680). (Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008).