Molecular recognition and docking algorithms.

By N. Brooijmans, Irwin D. Kuntz. 2003

724 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Physical and Theoretical Chemistry, Spectroscopy

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Citations in the corpus

End-to-end protein–ligand complex structure generation with diffusion-based generative models (2022, methodology): “Previous approaches predominantly employ the molecular docking methodology [2–8] that predicts preferred conformations of a ligand in a protein binding site.”
Virtual ligand screening: strategies, perspectives and limitations (2006, neutral): “These have been recently reviewed [96] [97] [98] [99] [100] [101] [102] .”
Virtual screening strategies in drug discovery: a critical review. (2013, background): “A critical step for the success of SBVS is the scoring of the ligands [65, 66].”
Flexible protein-protein docking. (2006, neutral): “!) and many of the developments that I report here have been previously implemented in protein–ligand docking (for an overview, see [2,3]).”
Virtual Screening with AutoDock: Theory and Practice (2010, background): “Building on 2 decades of research, many successful methods for docking of ligands to macromolecular targets have been developed [6-13].”
Advances and Challenges in Protein-Ligand Docking (2010, background): “Among them, protein-ligand docking is a particularly vibrant research area because of its importance to structure-based drug design [2–8] and will be the subject of the present review.”
Comparative evaluation of eight docking tools for docking and virtual screening accuracy (2004, methodology): “Docking small-molecular-weight ligands to therapeutically relevant macromolecules has become a major computational method for predicting protein–ligand interactions and guide lead optimization.(1) From the pioneering work of Kuntz et al.”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, methodology): “Given a target protein structure molecular docking samples hundreds or thousands of orientations or conformations of a ligand at the putative binding site, evaluates the energy score of each orientation/conformation, and ranks the orientations and conformations according to their scores.(1,2) The li”
Docking and scoring in virtual screening for drug discovery: methods and applications (2004, background): “In view of these challenges, docking is generally devised as a multi-step process in which each step introduces one or more additional degrees of complexit”