Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 1585-1587 |
| Number of pages | 3 |
| Journal | Bioinformatics |
| Volume | 35 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 1 May 2019 |
Funding
This work was supported by the European H2020 e-Infrastructure grants West-Life [grant no. 675858] and BioExcel [grant no. 675728], by the Dutch Foundation for Scientific Research (NWO) [TOP-PUNT grant 718.015.001] and the ASDI eScience grant [027016G04]. LX acknowledges financial support from the Netherlands Organization for Scientific Research [Veni grant 722.014.005]. C.G. acknowledges financial support from the China Scholarship Council [Grant No. 201406220132]. AV was supported by the Marie Skłodowska-Curie Individual Fellowship H2020 MSCA-IF-2015 [BAP-659025].