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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.
