TY - GEN
T1 - A computational pipeline for protein structure prediction and analysis at genome scale
AU - Shah, Manesh
AU - Passovets, Sergei
AU - Kim, Dongsup
AU - Ellrott, Kyle
AU - Wang, Li
AU - Vokler, Inna
AU - LoCascio, Philip
AU - Xu, Dong
AU - Xu, Ying
N1 - Publisher Copyright:
© 2013 IEEE.
PY - 2003
Y1 - 2003
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=0037852033&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0037852033&partnerID=8YFLogxK
U2 - 10.1109/BIBE.2003.1188923
DO - 10.1109/BIBE.2003.1188923
M3 - Conference contribution
AN - SCOPUS:0037852033
T3 - Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
SP - 3
EP - 10
BT - Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003
Y2 - 10 March 2003 through 12 March 2003
ER -