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On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure

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Summary

It is shown that the computer program LUDI can be used to search large databases of three-dimensional structures for putative ligands of proteins with known 3D structure. As an example, a subset of ≈30 000 small molecules (with less than 40 atoms and 0–2 rotatable bonds) from the Fine Chemicals Directory has been used in the search for possible novel ligands for four different proteins (trypsin, streptavidin, purine nucleoside phosphorylase and HIV protease). For trypsin and streptavidin, known ligands or substructures of known ligands are retrieved as top-scoring hits. In addition, a number of new interesting structures are found in all considered cases. Therefore, the method holds promise to retrieve automatically protein ligands from a 3D database if the 3D structure of the target protein is known.

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  1. Central Research, BASF AG, D-67056, Ludwigshafen, Germany

    Hans-Joachim Böhm

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Böhm, HJ. On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure. J Computer-Aided Mol Des 8, 623–632 (1994). https://doi.org/10.1007/BF00123669

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