ArticleNucleic acids research2016
CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- CLIMBS: Assessing Carbohydrate-Protein Interactions through a Graph Neural Network Classifier Using Synthetic Negative Data.Journal of chemical information and modeling · 2026Article
- Pharmaceutical Peptides: From Synthesis and Mechanistic Pharmacology to Future Biologic Therapeutics.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structures.Briefings in bioinformatics · 2026Article
- Extremely Randomized Trees to Determine Binding Affinity.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity.Current medicinal chemistry · 2025Review
- CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces.Proteins · 2025Article
- piscesCSM: prediction of anticancer synergistic drug combinations.Journal of cheminformatics · 2024Article
- AI-Driven Enhancements in Drug Screening and Optimization.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Computational toolbox for the analysis of protein-glycan interactions.Beilstein journal of organic chemistry · 2024Review
- PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity.Journal of cheminformatics · 2023Article
- Using Graph-Based Signatures to Guide Rational Antibody Engineering.Methods in molecular biology (Clifton, N.J.) · 2023Article
- kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors.Protein science : a publication of the Protein Society · 2022Article
- Evaluating hierarchical machine learning approaches to classify biological databases.Briefings in bioinformatics · 2022Article
- cropCSM: designing safe and potent herbicides with graph-based signatures.Briefings in bioinformatics · 2022Article
- Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures.Briefings in bioinformatics · 2022Article
- CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function.Briefings in bioinformatics · 2022Article
- Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach.Biophysical chemistry · 2021Article
- Artificial intelligence to deep learning: machine intelligence approach for drug discovery.Molecular diversity · 2021Review
- pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties.Journal of chemical information and modeling · 2021Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Determining the affinity of a ligand for a given protein is a crucial component of drug development and understanding their biological effects. Predicting binding affinities is a challenging and difficult task, and despite being regarded as poorly predictive, scoring functions play an important role in the analysis of molecular docking results. Here, we present CSM-Lig (http://structure.bioc.cam.ac.uk/csm_lig), a web server tailored to predict the binding affinity of a protein-small molecule complex, encompassing both protein and small-molecule complementarity in terms of shape and chemistry via graph-based structural signatures. CSM-Lig was trained and evaluated on different releases of the PDBbind databases, achieving a correlation of up to 0.86 on 10-fold cross validation and 0.80 in blind tests, performing as well as or better than other widely used methods. The web server allows users to rapidly and automatically predict binding affinities of collections of structures and assess the interactions made. We believe CSM-lig would be an invaluable tool for helping assess docking poses, the effects of multiple mutations, including insertions, deletions and alternative splicing events, in protein-small molecule affinity, unraveling important aspects that drive protein-compound recognition.
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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.