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Top 3 submissions, based on Kendall’s τ, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.
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1) Product Images from "D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings"

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings

Journal: Journal of computer-aided molecular design

doi: 10.1007/s10822-018-0180-4

Top 3 submissions, based on Kendall’s τ, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.
Figure Legend Snippet: Top 3 submissions, based on Kendall’s τ, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.

Techniques Used: Software

Top 3 submissions, based on Matthews correlation coefficient, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.
Figure Legend Snippet: Top 3 submissions, based on Matthews correlation coefficient, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.

Techniques Used: Software

Related Articles

Software:

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: Guo-Wei Michigan State University y7qxv 0.5 docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome.

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: Koes University of Pittsburgh 7bi2k 0.56 docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome.

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: Zou University of Missouri-Columbia fn2qt VEGFR2 0.53 docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via J. Sunseri/D.

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: 0.56 , docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome. , J. Sunseri/D. Koes , University of Pittsburgh , yghq5.

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: Zou University of Missouri-Columbia 87mci 0.23 docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome.

Article Title: A practical guide to machine-learning scoring for structure-based virtual screening.
Article Snippet: Structure-based virtual screening (SBVS) via docking has been used to discover active molecules for a range of therapeutic targets.. Chemical and protein data sets that contain integrated bioactivity information have increased both in number and in size.. Artificial intelligence and, more concretely, its machine-learning (ML) branch, including deep learning, have effectively exploited these data sets to build scoring functions (SFs) for SBVS against targets with an atomic-resolution 3D model (e.g., generated by X-ray crystallography or predicted by AlphaFold2).

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: 0.53 , docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via , J. Sunseri/D. Koes , University of Pittsburgh , 8civr.

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings
Article Snippet: 0.5 , docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome. , J. Sunseri/D. Koes , University of Pittsburgh , xpmn7.



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