Concepedia

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

Duc Duy Nguyen, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Ping Cao, Guo‐Wei Wei

Journal of Computer-Aided Molecular Design · 2018 · 164 citations · 63 references

Open access

Concepts

ComputingComputer ScienceMathematicsComputational ChemistryMachine LearningStructural BiologyBinding AffinityBinding Affinity PredictionDeep LearningMolecular DockingProtein-ligand DockingProtein-protein DockingBinding Pose PredictionLigand Binding Pose OptimizationLigand Pose PredictionPose PredictionPose RankingProtein-ligand Binding Affinity PredictionProtein-ligand Binding Pose Prediction

References

63

The Protein Data Bank

Helen M. Berman · Nucleic Acids Research · 2000 · 39.8K citations

Life Sciences, Biochemistry, Bioinformatics +10

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Oleg Trott, Arthur J. Olson · Journal of Computational Chemistry · 2009 · 37.1K citations · Full text

Pharmacy, Chemistry, Medicinal Chemistry +17

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Garrett M. Morris, Ruth Huey, William Lindstrom et al. · Journal of Computational Chemistry · 2009 · 25K citations · Full text

Pharmacy, Bioinformatics, Medicinal Chemistry +13

Centrality in social networks conceptual clarification

Linton C. Freeman · Social Networks · 1978 · 16.9K citations

Social Sciences, Sociology, Network Visualization +10

Open Babel: An open chemical toolbox

Noel M. O’Boyle, Michael Banck, Craig A. James et al. · Journal of Cheminformatics · 2011 · 11.1K citations · Full text

Natural Sciences, Chemistry, Computational Chemistry +9