Welcome to what I hope is a comprehensive list of startups using machine learning to research and develop drugs. I began this list in November 2017. At that time, it had 37 startups. I have updated it continuously since then. My focus is companies that (1) are new (I'm leaving this purposely vague, but typically founded post-2012); (2) use AI as a key differentiator; (3) develop products or drugs (I exclude service businesses); and (4) have demonstrated traction, such as via at least seed funding.
I group startups here roughly by R&D phase, though I don't use standard terminology (like target discovery, lead optimization, and so forth). This is because it wouldn't capture some of the nuances of what these companies do. For example, it would be harder to reflect the difference between companies repurposing drugs versus generating new molecular entities.