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GTC ON-DEMAND

Computational Biology & Chemistry
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Deep Learning for Molecular Docking
Abstract:
Molecular docking is an important tool for computational drug discovery that aims to predict the binding pose of a ligand (drug) to a target protein. Identifying a correctly oriented pose requires a scoring function that has a global optimum close to the experimentally observed pose. Additionally, it should also be differentiable with respect to atomic positions so that it can be used for gradient-based pose optimization. We'll describe a differentiable grid-based convolutional neural network scoring function and explore its application in an end-to-end GPU-optimized molecular docking workflow. We'll show that convolutional neural networks trained on experimental data can successfully identify correct binding modes and meaningfully rank and score compounds. We'll also describe several visualization approaches that map the CNN score back to the atomic inputs to help guide medicinal chemistry optimization and provide insight into the functioning of the neural network. The entirety of our approach is available under an open-source license as part of our gnina package (https://github.com/gnina).
 
Topics:
Computational Biology & Chemistry, Deep Learning & AI Frameworks
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8540
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