Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics

	This Article
	Subscribers, please Login Purchase article: $19 PDF IEEE Xplore Subscribers RSS feed
	Share
	Email this Article to a friend
	Bibliographic References
	ASCII Text BibTex RefWorks Procite/RefMan/Endnote
	Add to:
	Digg Furl Spurl Blink Simpy Google Del.icio.us Y!MyWeb
	Search
	Similar Articles Articles by M. Taufer Articles by M. Crowley Articles by D. Price Articles by A. A. Chien Articles by C. L. Brooks III

18th International Parallel and Distributed Processing Symposium (IPDPS'04) - Workshop 9

Santa Fe, New Mexico

April 26-April 30

ISBN: 0-7695-2132-0

	ASCII Text	x
	M. Taufer, M. Crowley, D. Price, A. A. Chien, C. L. Brooks III, "Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics," Parallel and Distributed Processing Symposium, International, vol. 10, pp. 188, 18th International Parallel and Distributed Processing Symposium (IPDPS'04) - Workshop 9, 2004.

	BibTex	x
	@article{ 10.1109/IPDPS.2004.1303203, author = {M. Taufer and M. Crowley and D. Price and A. A. Chien and C. L. Brooks III}, title = {Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics}, journal ={Parallel and Distributed Processing Symposium, International}, volume = {10}, year = {2004}, isbn = {0-7695-2132-0}, pages = {188}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2004.1303203}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Parallel and Distributed Processing Symposium, International TI - Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics SN - 0-7695-2132-0 SP EP A1 - M. Taufer, A1 - M. Crowley, A1 - D. Price, A1 - A. A. Chien, A1 - C. L. Brooks III, PY - 2004 KW - Force field based methods KW - docking accuracy KW - desktop grid computing VL - 10 JA - Parallel and Distributed Processing Symposium, International ER -

M. Taufer, University of California at San Diego, The Scripps Research Institute and Center for Theoretical Biological Physics

M. Crowley, The Scripps Research Institute

D. Price, The Scripps Research Institute

A. A. Chien, University of California at San Diego

C. L. Brooks III, The Scripps Research Institute and Center for Theoretical Biological Physics

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/IPDPS.2004.1303203

Few methods use molecular dynamics simulations based on atomically detailed force fields to study the protein-ligand docking process because they are considered too time demanding despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics simulations which has a highly flexible computational granularity. We compare the accuracy and the time required with well-known, commonly used docking methods like AutoDock, DOCK, FlexX, ICM, and GOLD. We show that our algorithm is accurate, fast and, because of its flexibility, applicable even to loosely coupled distributed systems like desktop grids for docking.

Index Terms:

Force field based methods, docking accuracy, desktop grid computing

Citation:

M. Taufer, M. Crowley, D. Price, A. A. Chien, C. L. Brooks III, "Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics," ipdps, vol. 10, pp.188, 18th International Parallel and Distributed Processing Symposium (IPDPS'04) - Workshop 9, 2004

Peer Review Notice | Give Us Feedback

Usage of this product signifies your acceptance of the Terms of Use.