EROS-DOCK — Protein-Protein Docking by Exhaustive Rotational Search
About EROS-DOCK
EROS-DOCK is an original coarse-grained docking approach that uses the physics-based ATTRACT scoring function in conjunction with a novel quaternion « pi-ball » representation of 3D rotational space. The pi-ball allows over 95% of candidate docking poses to be eliminated trivially due to steric clashes, thus allowing the remaining non-clashing orientations to be calculated very efficiently. In this way, the approach combines the exhaustive coverage of classical FFT-based approaches with an « exact » high quality scoring function.
EROS-DOCK was written by Maria Elisa Ruiz Echartea during her PhD Thesis , under the supervision of Dave Ritchie then Marie-Dominique Devignes, and the co-supervision of Isaure Chauvot de Beauchêne.
Download EROS-DOCK
- EROS-DOCK 2.1.4 (to be updated, currently not working)
EROS-DOCK Documentation and Examples
A README file and some examples are included in the distribution file.
References
The following publications describe the EROS-DOCK algorithm and its applications:
- EROS-DOCK: Protein-Protein Docking Using Exhaustive “Branch-and-Bound Rotational Search, Ruiz Echartea ME, Chauvot de Beauchene I, Ritchie DW. Bioinformatics 35:5003-5010, 2019. doi: 10.1093/bioinformatics/btz434.
- Using restraints in EROS-DOCK improves model quality in pairwise and multicomponent protein docking.Ruiz Echartea ME, Ritchie DW, Chauvot de Beauchêne I. Proteins 88:1121-1128, 2020. doi: 10.1002/prot.25959.
Acknowledgements
Dave Ritchie passed away prematurely on Sept 15, 2019. His open-mindedness and scientific contributions continue to inspire us.
Contact
Sjoerd de Vries
SISR LORIA
Campus Scientifique
BP239
54500 Vandoeuvre-lès-Nancy
sjoerd.devries AT loria.fr
