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Updated: Feb 2, 2026

Biochemical Reconstitution of Steroid Receptor•Hsp90 Protein Complexes and Reactivation of Ligand Binding
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Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand
Mikhail Ignatov1,2,3,4, Cong Liu2, Andrey Alekseenko5,4
1Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
Abstract:
Manifold representations of rotational/translational motion and conformational space of a ligand were previously shown to be effective for local energy optimization. In this paper we report the development of the Monte-Carlo energy minimization approach (MCM), which uses the same manifold representation. The approach was integrated into the docking pipeline developed for the current round of D3R experiment, and according to D3R assessment produced high accuracy poses for Cathepsin S ligands. Additionally, we have shown that (MD) refinement further improves docking quality. The code of the Monte-Carlo minimization is freely available at https://bitbucket.org/abc-group/mcm-demo .
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