Rapid Context-Dependent Ligand Desolvation in Molecular Docking

By Michael M. Mysinger, Brian K. Shoichet. 2010

316 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Issues such as desolvation and entropic effects are examples of the challenges to be overcome by the current docking algorithms [71,72].”
PotentialNet for Molecular Property Prediction (2018, methodology): “Methods like BEDROC 32 and LogAUC 33 weight the importance of the model’s highest performers more heavily.”
AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery (2015, positive): “Because the non-linearity of a logAUC value makes it hard to interpret, we subtract the area under the log-scaled random curve (0.14462) from a logAUC to get an adjusted-logAUC [38].”
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking (2012, methodology): “As described previously, 31 LogAUC is completely analogous to AUC but in the transformed space after you have zoomed in on early enrichment by taking the semilog of the x -axis.”
Performance of machine-learning scoring functions in structure-based virtual screening (2017, methodology): “Ligand 3D conformations were generated with three docking programs; AutoDock Vina (the Smina implementation, [http://smina.sf.net/]) 35,36 , Dock 3.6 37 and Dock 6.6 37–39 .”
Structure-based drug screening for G-protein-coupled receptors. (2012, methodology): “Widely used docking programs include AutoDock,[47] ICM,[48] FlexX,[49] Glide,[50] and DOCK.[51, 52] A web-based, automated version of the last is available at http://blaster.”
Ligand Pose and Orientational Sampling in Molecular Docking (2013, methodology): “In previous versions of DOCK3.x [79, 80, 93, 106] and ZINC [101, 102] , aromatic hydroxyl protons were usually placed in high-energy, incorrect conformations, out of the plane of the ring.”
The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery (2014, methodology): “…of the heme Soret band shift as before 37,39 Flexible Receptor Preparation DOCK 3.7 41 uses physics-based scoring consisting of van der Waals 42 and ligand desolvation terms 49 , combined with interaction electrostatic using a probe-charge implementation of the Poisson-Boltzmann equation.”
Latest developments in molecular docking: 2010–2011 in review (2013, methodology): “[75] Other methods To account for the dielectric permittivity variance between the protein (~2) and bulk water (~80), Garden and Zhorov proposed an atom – atom solvent exposure-dependent and distance-dependent dielectric function.”
A practical guide to large-scale docking (2021, background): “2) 17,77,79 – 81 metric to monitor the performance of a virtual screen by a single number 17 (Fig.”