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COACH-D 2.0: A Server for Template-based Modeling of Protein-ligand Interactions
Xiaoyu An1, Hong Wei2, Wenkai Wang1
1MOE Frontiers Science Center for Nonlinear Expectations, State Key Laboratory of Cryptography and Digital Economy Security, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China.
Genomics, Proteomics & Bioinformatics
|July 30, 2026
Summary
COACH-D 2.0 enhances protein-ligand binding site prediction using improved template-based methods. This new version boosts speed and accuracy for modeling protein complexes and interactions.
Area of Science:
- Computational Biology
- Structural Biology
- Drug Discovery
Background:
- Accurate protein-ligand interaction modeling is crucial but challenging.
- Template-based methods using homologous structures remain a vital strategy.
Purpose of the Study:
- To introduce COACH-D 2.0, an advanced template-based method for predicting protein-ligand binding sites.
- To improve prediction accuracy, speed, and the ability to model protein complexes.
Main Methods:
- Integrated multimeric templates from Q-BioLiP into an in-house library.
- Developed a new module for processing multimeric structures and predicting binding sites in complexes.
- Implemented an efficient template screening strategy.
Main Results:
- COACH-D 2.0 demonstrated superior performance compared to its previous version and leading methods.
- Significant improvements in both prediction speed and accuracy were achieved.
- Successfully enabled binding site prediction for protein complexes.
Conclusions:
- COACH-D 2.0 represents a substantial advancement in template-based protein-ligand binding site prediction.
- The enhanced method offers improved capabilities for modeling complex protein interactions.
- The freely accessible server facilitates research in structural biology and drug discovery.
Keywords:
Molecular dockingMonomeric structureMultimeric structureProtein−ligand interactionTemplate-based modelingMore Related Videos
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