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Molecular graphics to link structure to function

Paul Barrett and Martin Noble
Department of Biochemistry, University of Oxford, South Parks Road,
Oxford, OX1 3QU

One of the purposes of molecular graphics is to assist in understanding the relationship between protein structure and function. A current challenge in this area is presented by the generation and analysis of information about the character of motions that are likely to be explored by a protein structure, as inferred from molecular mechanical techniques.

We present a public, web-based facility to generate dynamic structural data for proteins, starting from a static structure (i.e. a PDB file). The computational techniques used to achieve this are well established but take time to learn. Our service means that researchers no longer need to learn these techniques if a simple dynamic analysis is all that they want. The user provides a protein coordinate file and clicks “start”. The dynamics of the protein are then simulated. The user subsequently downloads the simulation trajectory and associated analyses, such as animations and "principal component" summaries. The service will allow a much wider community to benefit from the functional insights that dynamic data provides.