ArticleProtein science : a publication of the Protein Society2022
BindWeb: A web server for ligand binding residue and pocket prediction from protein structures.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- CAPIM: Catalytic activity and site prediction and analysis tool in multimer proteins.Protein science : a publication of the Protein Society · 2025Article
- Computational Approaches for Discovering Virulence Factors inJournal of fungi (Basel, Switzerland) · 2025Review
- PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.Nucleic acids research · 2025Article
- BindWeb: A web server for ligand binding residue and pocket prediction from protein structures.Protein science : a publication of the Protein Society · 2022Article
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4 authors.
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Abstract
Knowledge of protein-ligand interactions is beneficial for biological process analysis and drug design. Given the complexity of the interactions and the inadequacy of experimental data, accurate ligand binding residue and pocket prediction remains challenging. In this study, we introduce an easy-to-use web server BindWeb for ligand-specific and ligand-general binding residue and pocket prediction from protein structures. BindWeb integrates a graph neural network GraphBind with a hybrid convolutional neural network and bidirectional long short-term memory network DELIA to identify binding residues. Furthermore, BindWeb clusters the predicted binding residues to binding pockets with mean shift clustering. The experimental results and case study demonstrate that BindWeb benefits from the complementarity of two base methods. BindWeb is freely available for academic use at http://www.csbio.sjtu.edu.cn/bioinf/BindWeb/.
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