FRED Pose Prediction and Virtual Screening Accuracy
By Mark McGann. Journal of Chemical Information and Modeling, 2011
682 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3b4edff043bec84a1e02b67139e6fb6e8efd06fb
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In Computational Theory and Mathematics
- Tommi S. Jaakkola
- Regina Barzilay
- Brian K. Shoichet
- John J. Irwin
- John Karanicolas
- Teague Sterling
- Connor W. Coley
- Ryan G. Coleman
In Molecular Biology
- Tommi S. Jaakkola
- Regina Barzilay
- John J. Irwin
- Brian K. Shoichet
- John Karanicolas
- Teague Sterling
- Ryan G. Coleman
- Michael Carchia
Citations in the corpus
- Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases (2018, neutral): “Some of the most commonly used docking tools are AutoDock [42], DOCK [43], Glide [44], GOLD [45], FlexX [46] and Fred [47].”
- Fast Docking on Graphics Processing Units via Ray-Casting (2013, background): “While some methods allow the ligand conformation to vary during docking [9,12,13], others carry out independent docking trajectories using a series of pre-built low-energy ligand conformations (‘‘conformers’’) [7,14,15].”
- Docking and scoring with ICM: the benchmarking results and strategies for improvement (2012, methodology): “Target sites of approximately the same size but different families were matched as described by McGann [46] and their ligands included in the annotated sdf file for docking.”
- Ligand Pose and Orientational Sampling in Molecular Docking (2013, methodology): “The program FRED[69] exhaustively samples geometries defined by a”
- Latest developments in molecular docking: 2010–2011 in review (2013, methodology): “N o s u c h j u d g m e n t w a s m a d e i n [ 90 ] .”
- GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles (2021, background): “…2018, Klicpera et al., 2019, Axelrod and Gomez-Bombarelli, 2020b, Schütt et al., 2021] such as charge distribution, potential energy, docking poses [McGann, 2011], shape similarity [Kumar and Zhang, 2018], pharmacophore searching [Schwab, 2010], or descriptors for 3/4D QSAR [Verma et al., 2010].”