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Michela Taufer, M Crowley, D Price, Andrew Chien, and C L III (2004)

Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics

In: Proceedings of the Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), IEEE Press.

Few methods use molecular dynamics simulations based on atomically detailed force fields to study the proteinligand 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.

Held in conjunction with IPDPS 2004, Santa Fe, New Mexico, April 2004.
by admin last modified 2009-11-04 07:05
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