Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server

Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared wi...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2019-05, Vol.35 (9), p.1585-1587
Main Authors: Vangone, Anna, Schaarschmidt, Joerg, Koukos, Panagiotis, Geng, Cunliang, Citro, Nevia, Trellet, Mikael E, Xue, Li C, Bonvin, Alexandre M J J
Format: Article
Language:English
Subjects:
Binding Sites
Computers
Internet
Ligands
Protein Binding
Protein Conformation
Software
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Summary:Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here we present an extension of it, named PRODIGY-LIG, aimed at the prediction of affinity in protein-small ligand complexes. The predictive method, properly readapted for small ligand by making use of atomic instead of residue contacts, has been successfully applied for the blind prediction of 102 protein-ligand complexes during the D3R Grand Challenge 2. PRODIGY-LIG has the advantage of being simple, generic and applicable to any kind of protein-ligand complex. It provides an automatic, fast and user-friendly tool ensuring broad accessibility. PRODIGY-LIG is freely available without registration requirements at http://milou.science.uu.nl/services/PRODIGY-LIG.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/bty816