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| About Robin Taylor (CCDC) |
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Robin Taylor has worked for the Cambridge Crystallographic Data Centre (CCDC) for twelve years. He leads the software group which is responsible for the development of widely-used programs such as GOLD, Relibase+, ConQuest, Mogul and IsoStar. Prior to joining CCDC, he was Group Leader of the Computational Chemistry Group at Zeneca Agrochemicals, and before that he had several years in academia. He has a long-standing interest in using crystal-structure databases to facilitate the rational design of biologically-active molecules.
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Dealing with Active Site Plasticity using GOLD
Robin Taylor, Cambridge Crystallographic Data Centre
For many proteins, side chain and loop movements and active site bound water play an important role in determining a ligand’s affinity. Yet evaluating these influences quickly in a time frame compatible with swift processing of structures is not trivial. Consequently it is only recently that docking programs have started to consider protein flexibility and treatment of water.
The docking program GOLD has recently been enhanced to accommodate local side-chain movements and small changes in the positions of Calpha atoms. GOLD is also capable of assessing whether active site water should be retained or excluded in the top ranking dockings. Both these enhancements have been achieved without greatly increasing the search time required. The methodology behind these advances and validation results will be presented.
Gross movements within the active site are more difficult to take account of during a docking run. One approach is to dock against several different protein molecules and then analyse the results to select out the most favoured binding ligands. We will demonstrate how these analyses and other post-docking processing tasks may be carried out using the analysis program GoldMine.
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