Abstract Few methods use molecular dynamics simulations in concert with atomically detailed force fields to perform protein–ligand docking calculations because they are considered too time demanding, despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics which has a highly flexible computational granularity. We compare the accuracy and the time required with well‐known, commonly used docking methods such as 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 such as desktop Grids for docking. Copyright © 2005 John Wiley & Sons, Ltd.

Summary form only given. 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. 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.

Abstract One benefit of a computational Grid is the ability to run high‐performance applications over distributed resources simply and securely. We demonstrated this benefit with an experiment in which we studied the protein‐folding process with the CHARMM molecular simulation package over a Grid managed by Legion, a Grid operating system. High‐performance applications can take advantage of Grid resources if the Grid operating system provides both low‐level functionality as well as high‐level services. We describe the nature of services provided by Legion for high‐performance applications. Our experiences indicate that human factors continue to play a crucial role in the configuration of Grid resources, underlying resources can be problematic, Grid services must tolerate underlying problems or inform the user, and high‐level services must continue to evolve to meet user requirements. Our experiment not only helped a scientist perform an important study, but also showed the viability of an integrated approach such as Legion's for managing a Grid. Copyright © 2004 John Wiley & Sons, Ltd.

One benefit of a computational grid is the ability to run high-performance applications over distributed resources simply and securely. We demonstrate this benefit with an experiment in which we studied the protein folding process with the CHARMM molecular simulation package over a grid managed by Legion, a grid operating system. High-performance applications can take advantage of grid resources if the grid operating system provides both low level functionality as well as high-level services. We describe the nature of services provided by Legion for high-performance applications. Our experiences indicate that human factors continue to play a crucial role in the configuration of grid resources, underlying resources can be problematic, grid services must tolerate underlying problems or inform the user, and high-level services must continue to evolve to meet user requirements. Our experiment not only helped a scientist perform an important study, but also showed the viability of an integrated approach such as Legion's for managing a grid.