  A major challenge in computational chemistry is the generation of novel
molecular structures with desirable pharmacological and physiochemical
properties. In this work, we investigate the potential use of autoencoder, a
deep learning methodology, for de novo molecular design. Various generative
autoencoders were used to map molecule structures into a continuous latent
space and vice versa and their performance as structure generator was assessed.
Our results show that the latent space preserves chemical similarity principle
and thus can be used for the generation of analogue structures. Furthermore,
the latent space created by autoencoders were searched systematically to
generate novel compounds with predicted activity against dopamine receptor type
2 and compounds similar to known active compounds not included in the training
set were identified.
