ArticleJournal of computer-aided molecular design2020
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.
Article in Journal of computer-aided molecular design, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.Proteins · 2026Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- Template-guided method for protein-ligand complex structure prediction: Application to CASP15 protein-ligand studies.Proteins · 2023Article
- Article
- High Accuracy Prediction of PROTAC Complex Structures.Journal of the American Chemical Society · 2023Article
- Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions.Journal of chemical information and modeling · 2022Review
- Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2.Molecular cell · 2020Article
- Protein storytelling through physics.Science (New York, N.Y.) · 2020Review
- ClusPro LigTBM: Automated Template-based Small Molecule Docking.Journal of molecular biology · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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.
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Registered trials
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