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      Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

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          Abstract

          We describe a new template-based method for docking flexible ligands such as macrocycles to proteins. It combines Monte-Carlo energy minimization on the manifold (MCMM), a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics (MD) simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource (D3R) blind Grand Challenge competition. This method was among the best performers in the competition, giving sub-angstrom prediction quality for the majority of the targets.

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          AMBER 2016 reference manual

           DA Case (2016)
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            Author and article information

            Contributors
            Journal
            Journal of Computer-Aided Molecular Design
            J Comput Aided Mol Des
            Springer Science and Business Media LLC
            0920-654X
            1573-4951
            February 2020
            December 26 2019
            February 2020
            : 34
            : 2
            : 179-189
            Article
            10.1007/s10822-019-00257-1
            7553231
            31879831
            © 2020

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