Abstract
Three categories of molecular flexibility are defined. A novel method ofaligning partly flexible molecules with each other is described. The bindingmode of one of these molecules to its receptor site was already well knownfrom previous crystallographic studies, and this known binding mode was usedto predict the binding mode of the other molecules at their receptor. Thepredictions were checked by comparison with previous observations, and werecorrect. Two novel methods were combined in this research. It was necessaryto take account of the conformational changes which occur when each ligandmolecule binds to the protein, and a new release of programme Grid was usedfor this. It was also necessary to analyse the Grid results in order todistinguish the role of each chemical group at the receptor site. This wasdone by applying hierarchical principal component analysis (Hi-PCA) methodsto the descriptors obtained from Grid.
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Berglund, A., Rosa, M.C.D. & Wold, S. Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA. J Comput Aided Mol Des 11, 601–612 (1997). https://doi.org/10.1023/A:1007983320854
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DOI: https://doi.org/10.1023/A:1007983320854