Molecular motions in drug design: the coming age of the metadynamics method |
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Authors: | Xevi Biarnés Salvatore Bongarzone Attilio Vittorio Vargiu Paolo Carloni Paolo Ruggerone |
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Institution: | 1.International School for Advanced Studies,Trieste,Italy;2.Istituto Officina dei Materiali del CNR—Unità SLACS,Cagliari,Italy;3.Department of Physics,University of Cagliari,Cagliari,Italy;4.German Research School,Julich Research Center, Julich and RWTH,Aachen,Germany |
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Abstract: | Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also
to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method,
we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when
combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation,
may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity,
such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating
the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental
data. |
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