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2021_GNNs_for_Molecules.pdf
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2021_GNNs_for_Molecules
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Department of Computer Science & Engineering
Molecule Analysis
Yi Liu
Department of Computer Science & Engineering
1
Based on materials by Yi Liu and Shuiwang Ji
2
Some slides are adapted from Meng Liu (TAMU) and Stanford CS224W class
Department of Computer Science & Engineering
Outline
• Motivation
• Data & Problem Formulation
• Approach: Message Passing Perspective
• Advanced Topic: Molecular Conformation
• Resources and Libraries
Department of Computer Science & Engineering
Motivation
Department of Computer Science & Engineering
An Exemplary Problem
Ruddigkeit Lars, et al. “ Enumeration of 166 billion organic small
molecules in the chemical universe database GDB-17." J. Chem.
Inf. Model. 2012.
Department of Computer Science & Engineering
Approach: DFT
• Classic physical methods which could date back to 1960s.
• Key proposal of DFT is that the molecular properties are
determined by functionals of the spatially dependent electron
density. Hence, atomic locations are combined with quantum
mechanics to predict properties of molecules
• Pros:
– Accurate
– Widely used
• Cons:
– Extremely time consuming
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