ArticleNucleic acids research2025
LIGYSIS-web: a resource for the analysis of protein-ligand binding sites.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed.
- EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology.Patterns (New York, N.Y.) · 2026Article
- Decoding the allosteric grammar of protein kinases: A dual-stream framework integrating protein language models and energy landscape frustration analysis.Protein science : a publication of the Protein Society · 2026Article
- Predicting and Decoding Allosteric Binding Sites Using Protein Language Models and Structure-Based Machine Learning: An Energy Landscape-Guided Explainable AI Framework.Journal of chemical theory and computation · 2026Article
- EMERALD-UI: an interactive web application to unveil novel protein biology hidden in the alternative alignment space.Bioinformatics (Oxford, England) · 2026Article
- SwinSite: 3D Structure-Based Prediction of Protein-Ligand Binding Sites Using a Combined Vision Transformer and Convolution Model.Journal of chemical information and modeling · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
LIGYSIS-web is a free website accessible to all users without any login requirement for the analysis of protein-ligand binding sites. LIGYSIS-web hosts a database of 65,000 protein-ligand binding sites across 25,000 proteins. LIGYSIS sites are defined by aggregating unique relevant protein-ligand interfaces across different biological assemblies of the same protein deposited on the PDBe. Additionally, users can upload their own structures in PDB or mmCIF format for analysis and subsequent visualisation and download. Ligand sites are characterised using evolutionary divergence from a multiple sequence alignment, human missense genetic variation from gnomAD and relative solvent accessibility to obtain accessibility-based cluster labels and scores indicating likelihood of function. These results are displayed in the LIGYSIS web server, a Python Flask web application with a JavaScript frontend employing Jinja and jQuery to link the 3Dmol.js structure viewer with dynamic tables and Chart.js graphs in an interactive manner. LIGYSIS-web is available at https://www.compbio.dundee.ac.uk/ligysis/, whilst the source code for the analysis pipelines and web application can be accessed at https://github.com/bartongroup/LIGYSIS, https://github.com/bartongroup/LIGYSIS-custom and https://github.com/bartongroup/LIGYSIS-web, respectively.
Indexed as
Identifiers
What OpenQuestion holds
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.