期刊
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
卷 34, 期 2, 页码 179-189出版社
SPRINGER
DOI: 10.1007/s10822-019-00257-1
关键词
D3R; Protein-ligand docking; Template-based docking; Macrocycles; BACE-1
资金
- National Institutes of Health [R21 GM127952, 1R01GM125813-01]
- National Science Foundation [AF 1816314, AF 1645512, DBI 1759277, OCI-0725070, ACI-1238993]
- National Science Foundation PRAC Award [ACI-1713695]
- state of Illinois
- Division of Computing and Communication Foundations [AF 1816314]
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.
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