Molecular structure determination on a computational and data Grid

The focus of this paper is on the design and implementation of a critical program in structural biology onto two computational and data Grids. The first is the Buffalo-based ACDC Grid, which uses facilities at SUNY-Buffalo and several research institutions that are under distinct control. The second is Grid2003, the iVDGL Grid established late in 2003 primarily for physics and astronomy applications. In this paper, we prevent an overview of the ACDC Grid and Grid2003, focusing on the implementation of several new ACDC computational and Grid tools.

1. Introduction

The ACDC-Grid [11], [20], [21] is a proof-of-concept grid implemented in Buffalo, NY. The driving structural biology application provides a cost-effective solution to the problem of determining molecular structures from X-ray crystallographic data via the Shake-and-Bake direct methods procedure. SnB [1], a computer program based on the Shake-and-Bake method [2], [3], is the program of choice for structure determination in many of the 500 laboratories that have acquired it [4], [5], [6]. This computationally-intensive procedure can exploit the grid's ability to present the user with a large computational infrastructure that will allow for the processing of a large number of related molecular trial structures [7], [8].