MOTIVATION: Antibodies are currently the most important class of biopharmaceuticals. Development of such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques such as antibody-antigen docking hold the potential to facilitate the screening process by rapidly providing a list of initial poses that approximate the native complex. RESULTS: We have developed a new method to identify the epitope region on the antigen, given the structures of the antibody and the antigen-EpiPred. The method combines conformational matching of the antibody-antigen structures and a specific antibody-antigen score. We have tested the method on both a large non-redundant set of antibody-antigen complexes and on homology models of the antibodies and/or the unbound antigen structure. On a non-redundant test set, our epitope prediction method achieves 44% recall at 14% precision against 23% recall at 14% precision for a background random distribution. We use our epitope predictions to rescore the global docking results of two rigid-body docking algorithms: ZDOCK and ClusPro. In both cases including our epitope, prediction increases the number of near-native poses found among the top decoys. AVAILABILITY AND IMPLEMENTATION: Our software is available from http://www.stats.ox.ac.uk/research/proteins/resources.

The concept of GRASS (Geographic Resources Analysis Support System) as an open system has created a favourable environment for integration of process based modelling and GIS. To support this integration a new generation of tools is being developed in the following areas: (a) interpolation from multidimensional scattered point data, (b) analysis of surfaces and hypersurfaces, (c) modelling of spatial processes and, (d) 3D dynamic visualization. Examples of two applications are given-spatial and temporal modelling of erosion and deposition, and multivariate interpolation and visualization of nitrogen concentrations in the Chesapeake Bay.