Journal
FEBS LETTERS
Volume 580, Issue 22, Pages 5130-5136Publisher
WILEY
DOI: 10.1016/j.febslet.2006.08.037
Keywords
matrix metalloproteinases; MMPs; normal mode analysis (NMA); docking; target flexibility
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We demonstrate the utility of normal mode analysis in correctly predicting the binding modes of inhibitors in the active sites of matrix metalloproteinases (MMPs). We show the accuracy in predicting the positions of MMP-3 inhibitors is strongly dependent on which structure is used as the target, especially when it has been energy minimized. This dependency can be overcome by using intermediate structures generated along one of the normal modes previously calculated for a given target. These results may be of prime importance for further in silico drug discovery. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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