What is MedusaDock?
MedusaDock 2.0 is a protein-ligand docking method and web server.
It takes a protein structure or binding pocket as input, uses a constraint-aware docking workflow to improve sampling efficiency, and returns docked poses together with downloadable structure and log files.
MedusaDock 2.0 is designed to improve docking accuracy and efficiency by incorporating structural constraints from experiment or prediction while sampling ligand and receptor conformations.
How to cite the workflow
If you use this workflow in a publication, cite the papers below.
Wang J, Dokholyan NV. MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking with Constraints.
J Chem Inf Model. 2019;59(6):2509-2515. DOI: 10.1021/acs.jcim.8b00905
Ding F, Yin S, Dokholyan NV. Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands.
J Chem Inf Model. 2010;50(9):1623-1632. DOI: 10.1021/ci100218t
Ding F, Dokholyan NV. Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark.
J Chem Inf Model. 2013;53(8):1871-1879. DOI: 10.1021/ci300478y