Please take time to fill in the Annual BioExcel survey which contains a section about HADDOCK.
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To cite this service, please refer to:

  1. R.V. Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin "Structural biology in the clouds: The WeNMR-EOSC Ecosystem". Frontiers Mol. Biosci., 8, 10.3389/fmolb.2021.729513 (2021).

To cite PRODIGY, please refer to:

  1. Vangone A. and Bonvin A.M.J.J. "Contact-based prediction of binding affinity in protein-protein complexes", eLife, 4, e07454 (2015).
  2. Xue L., Rodrigues J., Kastritis P., Bonvin A.M.J.J.*, Vangone A.*, "PRODIGY: a web-server for predicting the binding affinity in protein-protein complexes", Bioinformatics, doi:10.1093/bioinformatics/btw514 (2016).

To cite PRODIGY-LIGAND, please refer to:

  1. Vangone A., Schaarschmidt J., Koukos P., Geng C., Citro N., Trellet M.E., Xue L., Bonvin A.M.J.J. “Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server”, Bioinformatics, bty816,
  2. Kurkcuoglu Z., Koukos P.I., Citro N., Trellet M.E., Rodrigues J.P.G.L.M., Moreira I.S., Roel-Touris J., Melquiond A.S.J., Geng C., Schaarschmidt J., Xue L.C., Vangone A. and Bonvin A.M.J.J. "Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2". J. Comp. Aid. Mol. Des.32, 175-185 (2018).

To cite PRODIGY-CRYSTAL, please refer to:

  1. Elez K., Bonvin A.M.J.J. and Vangone A."Distinguishing crystallographic from biological interfaces in protein complexes: Role of intermolecular contacts and energetics for classification", BMC Bioinformatics, 19 (Suppl 15) :438 (2018).
  2. Jiménez-García B., Elez K., Koukos P.I., Bonvin A.M.J.J. and Vangone A. "PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes", Bioinformatics, btz437 (2019).