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The Gray lab develops protein-protein docking software, relevant for the prediction of binding specificity. We published studies on HIV-1 protease specificity for cleavable and non-cleavable substrate peptides. We have continued to improve the docking software, in particular focusing on the effect of backbone conformational change, the incorporation on non-canonical and post-translationally modified amino acids, the effect of solution pH, and search strategies and scoring functions. Recent applications have included ubiquitin conjugating enzymes, uracil DNA glycosylase, camelid antibodies, and the AraC transcription factor.
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