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

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, a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource 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.

SUBMITTER: Kotelnikov S 

PROVIDER: S-EPMC7553231 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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

Kotelnikov Sergei S   Alekseenko Andrey A   Liu Cong C   Ignatov Mikhail M   Padhorny Dzmitry D   Brini Emiliano E   Lukin Mark M   Coutsias Evangelos E   Dill Ken A KA   Kozakov Dima D  

Journal of computer-aided molecular design 20191226 2

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, a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource blind Grand Challenge competition. This method was among the best performers in th  ...[more]

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