Stuart E. Murdock

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BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.
In computational biomolecular research, large amounts of simulation data are generated to capture the motion of proteins. These massive simulation data can be analysed in a number of ways to reveal the biochemical properties of the proteins. However, the legacy way of storing these data (usually in the laboratory where the simulations have been run) often(More)
Biomolecular simulations provide data on the conformational dynamics and energetics of complex biomolecular systems. We aim to exploit the e-science infrastructure developing in the UK to enable large scale analysis of the results of such simulations. In particular, the BioSimGrid project ( will provide a generic database for comparative(More)
The overall aim of the BioSimGrid project ( is to exploit the grid infrastructure to enable comparative analysis of the results of biomolecular simulations. In particular, we present the implementation of current BioSimGrid Web portal. The portal has a SOA (service oriented architecture) framework built on the layer of OGSA (open grid(More)
Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed(More)
Contemporary structural biology has an increased emphasis on high-throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance(More)
BioSimGrid aims to deliver a biomolecular simulation data repository to enable more efficient storage, access and exchange of biomolecular simulation data. This is an ongoing project still in development that seeks to exploit the concept of the Grid where large computational and data resources are made available to users in a highly accessible manner. The(More)
Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid ( database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely(More)
Using the concepts of publication@source technology, the data obtained from a range of spectroscopy and surface tension experiments, and that obtained from a number of related large computational simulations, have been stored in such a way as to enable a viewer to trace back through the analysis methods to the raw data. The storage of the simulation data is(More)
The overall aim of the BioSimGrid project ( is to exploit the Grid infrastructure to enable comparative analysis of the results of biomolecular simulations. In particular this paper discusses the security implementation of the BioSimGrid web portal. To achieve a secured application environment, a dedicated security layer has been built on(More)