  Predicting the biological function of molecules, be it proteins or drug-like
compounds, from their atomic structure is an important and long-standing
problem. Function is dictated by structure, since it is by spatial interactions
that molecules interact with each other, both in terms of steric
complementarity, as well as intermolecular forces. Thus, the electron density
field and electrostatic potential field of a molecule contain the "raw
fingerprint" of how this molecule can fit to binding partners. In this paper,
we show that deep learning can predict biological function of molecules
directly from their raw 3D approximated electron density and electrostatic
potential fields. Protein function based on EC numbers is predicted from the
approximated electron density field. In another experiment, the activity of
small molecules is predicted with quality comparable to state-of-the-art
descriptor-based methods. We propose several alternative computational models
for the GPU with different memory and runtime requirements for different sizes
of molecules and of databases. We also propose application-specific
multi-channel data representations. With future improvements of training
datasets and neural network settings in combination with complementary
information sources (sequence, genomic context, expression level), deep
learning can be expected to show its generalization power and revolutionize the
field of molecular function prediction.
