RosettaLigand docking with full ligand and receptor flexibility.

By Ian W Davis, David Baker. 2009

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State-specific protein–ligand complex structure prediction with a multiscale deep generative model (2022, positive): “We have also compared our quantitative results against a baseline method, RosettaLigand 40 , an algorithm designed for ligand docking with fast energy-based flexible receptor relaxation (Fig.”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, neutral): “…with a known structure (Gray et al. , 2003; Wang et al. , 2005) ligand_docking Predict the orientation that a small molecule binds to a protein (Davis and Baker, 2009; Kaufmann et al. , 2008; Meiler and Baker, 2006) loop_modeling Predict the conformation of a set of protein loops (Mandell et…”