A computational pipeline for protein structure prediction and analysis at genome scale

Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip LoCascio, Dong Xu, Ying Xu

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

2 Citations (Scopus)

Abstract

Traditionally, protein 3D structures are solved using experimental techniques, like x-ray crystallography or nuclear magnetic resonance (NMR). While these experimental techniques have been the main workhorse for protein structure studies in the past few decades, it is becoming increasingly apparent that they alone cannot keep up with the production rate of protein sequences. Fortunately, computational techniques for protein structure predictions have matured to such a level that they can complement the existing experimental techniques. In this paper, we present an automated pipeline for protein structure prediction. The centerpiece of the pipeline is a threading-based protein structure prediction system, called PROSPECT, which we have been developing for the past few years. The pipeline consists of seven logical phases, utilizing a dozen tools. The pipeline has been implemented to run in a heterogeneous computational environment as a client/server system with a web interface. A number of genome-scale applications have been carried out on microbial genomes. Here we present one genome-scale application on Caenorhabditis elegans.

Original languageEnglish (US)
Title of host publicationProceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages3-10
Number of pages8
ISBN (Print)0769519075, 9780769519074
DOIs
StatePublished - 2003
Externally publishedYes
Event3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003 - Bethesda, United States
Duration: Mar 10 2003Mar 12 2003

Other

Other3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
CountryUnited States
CityBethesda
Period3/10/033/12/03

Fingerprint

Pipelines
Genes
Proteins
Crystallography
Interfaces (computer)
Computer systems
Servers
Nuclear magnetic resonance
X rays

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Signal Processing
  • Electrical and Electronic Engineering

Cite this

Shah, M., Passovets, S., Kim, D., Ellrott, K., Wang, L., Vokler, I., ... Xu, Y. (2003). A computational pipeline for protein structure prediction and analysis at genome scale. In Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003 (pp. 3-10). [1188923] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2003.1188923

A computational pipeline for protein structure prediction and analysis at genome scale. / Shah, Manesh; Passovets, Sergei; Kim, Dongsup; Ellrott, Kyle; Wang, Li; Vokler, Inna; LoCascio, Philip; Xu, Dong; Xu, Ying.

Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 3-10 1188923.

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

Shah, M, Passovets, S, Kim, D, Ellrott, K, Wang, L, Vokler, I, LoCascio, P, Xu, D & Xu, Y 2003, A computational pipeline for protein structure prediction and analysis at genome scale. in Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003., 1188923, Institute of Electrical and Electronics Engineers Inc., pp. 3-10, 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003, Bethesda, United States, 3/10/03. https://doi.org/10.1109/BIBE.2003.1188923
Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I et al. A computational pipeline for protein structure prediction and analysis at genome scale. In Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 3-10. 1188923 https://doi.org/10.1109/BIBE.2003.1188923
Shah, Manesh ; Passovets, Sergei ; Kim, Dongsup ; Ellrott, Kyle ; Wang, Li ; Vokler, Inna ; LoCascio, Philip ; Xu, Dong ; Xu, Ying. / A computational pipeline for protein structure prediction and analysis at genome scale. Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 3-10
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