ArticleJournal of molecular biology2020
ClusPro LigTBM: Automated Template-based Small Molecule Docking.
Article in Journal of molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.Proteins · 2026Article
- Polaris Challenge: Data-Driven Priors to Improve Docking for Pose Prediction.Journal of chemical information and modeling · 2025Article
- TEMPL: A Template-Based Protein-Ligand Pose Prediction Baseline.Journal of chemical information and modeling · 2025Article
- DockOpt: A Tool for Automatic Optimization of Docking Models.Journal of chemical information and modeling · 2024Article
- Article
- High Accuracy Prediction of PROTAC Complex Structures.Journal of the American Chemical Society · 2023Article
- Integrated metabolomics and proteomics reveal biomarkers associated with hemodialysis in end-stage kidney disease.Frontiers in pharmacology · 2023Article
- Preclinical testing of dabigatran in trypsin-dependent pancreatitis.JCI insight · 2022Article
- Public Data Set of Protein-Ligand Dissociation Kinetic Constants for Quantitative Structure-Kinetics Relationship Studies.ACS omega · 2022Article
- Machine learning assessment of the binding region as a tool for more efficient computational receptor-ligand docking.Journal of molecular liquids · 2022Article
- Article
- Conservation of binding properties in protein models.Computational and structural biotechnology journal · 2021Article
- Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2.Molecular cell · 2020Article
- Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs.Marine drugs · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The template-based approach has been essential for achieving high-quality models in the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predicted Interactions). However, few such automated methods exist for protein-small molecule docking. In this paper, we present an algorithm for template-based docking of small molecules. It searches for known complexes with ligands that have partial coverage of the target ligand, performs conformational sampling and template-guided energy refinement to produce a variety of possible poses, and then scores the refined poses. The algorithm is available as the automated ClusPro LigTBM server. It allows the user to specify the target protein as a PDB file and the ligand as a SMILES string. The server then searches for templates and uses them for docking, presenting the user with top-scoring poses and their confidence scores. The method is tested on the Astex Diverse benchmark, as well as on the targets from the last round of the D3R (Drug Design Data Resource) Grand Challenge. The server is publicly available as part of the ClusPro docking server suite at https://ligtbm.cluspro.org/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.