A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction |
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Authors: | Brice Hoffmann Mikhail Zaslavskiy Véronique Stoven |
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Institution: | (1) Mines ParisTech, Centre for Computational Biology, 35 rue Saint Honore, Fontainbleau, F-77300, France;(2) Centre for Mathematical Morphology, 35 rue Saint Honore, Fontainebleau, F-77300, France;(3) Institut Curie, Paris, F-75248, France;(4) INSERM U900, Paris, F-75248, France |
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Abstract: | Background Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher
the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar
3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display
any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively
assessing the similarity between binding sites may therefore be useful to propose new ligands for a given pocket, based on
those known for similar pockets. |
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