Paul W. Fitzjohn

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Comparative modelling of proteins is a predictive technique to build an atomic model for a given amino acid sequence, on the basis of the structures of other proteins (templates) that have been determined experimentally. Critical problems arise in this procedure: selecting the correct templates, aligning the query sequence with them and building the(More)
The gap between the number of protein sequences and protein structures is increasing rapidly, exacerbated by the completion of numerous genome projects now flooding into public databases. To fill this gap, comparative protein modelling is widely considered the most accurate technique for predicting the three-dimensional shape of proteins. High-throughput,(More)
We have submitted models for all 9 targets in Rounds 3-5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid-body docking with a variety of initial(More)
A novel genetic algorithm was applied to all CASP5 targets. The algorithm simultaneously searches template and alignment space. Results show that the current implementation of the method is perhaps most useful in recognizing and refining remote homology targets. This new method is briefly described and results are analyzed. Strengths and weaknesses of the(More)
MOTIVATION A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different(More)
BACKGROUND Simulation methods can assist in describing and understanding complex networks of interacting proteins, providing fresh insights into the function and regulation of biological systems. Recent studies have investigated such processes by explicitly modelling the diffusion and interactions of individual molecules. In these approaches, two entities(More)
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