LIGYSIS-web: a resource for the analysis of protein-ligand binding sites

Nucleic Acids Res. 2025 May 16:gkaf411. doi: 10.1093/nar/gkaf411. Online ahead of print.

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.

PMID:40377089 | DOI:10.1093/nar/gkaf411