ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

By Jens Meiler, David Baker. 2006

483 citations recorded by the source corpus.

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Citations in the corpus

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “…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 al. , 2009; Rohl et al. , 2004) rna_denovo…”
Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery (2022, unknown): “…modeling (Hecker et al., 2002; Acharya et al., 2011; Vlachakis et al., 2015), structure-based (SB) protein-ligand docking (Friesner et al., 2004; Meiler and Baker, 2006; Davis and Baker, 2009; Hartmann et al., 2009; Morris et al., 2009; Kaufmann and Meiler, 2012; Lemmon et al., 2012), and…”
Computational Methods in Drug Discovery (2014, methodology): “ROSETTALIGAND was used by Kaufmann et al. (2009) to predict the binding mode of serotonin with serotonin transporters.”
Computational approaches streamlining drug discovery (2023, methodology): “The docking procedure itself can use molecular mechanics, often in internal coordinate representation, for rapid conformational sampling of fully flexible ligands 52,53 , using empirical 3D shape-matching approaches 54,55 , or combining them in a hybrid docking funnel 56,57 .”
New algorithms and an in silico benchmark for computational enzyme design (2006, background): “This potential has performed very well in protein– docking calculations (Meiler and Baker 2006).”
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011, background): “RosettaLigand allows the simultaneous sampling of protein, ligand, and rigid-body degrees of freedom”