Benjamin J. Shields, Ph.D.

Benjamin J. Shields, Ph.D.

Chemist & Machine Learning Engineer

New Series: Using And Building Agentic Systems For Cheminformatics

less than 1 minute read

Published:

Hello (again) world! After a few years away, I’m back to writing—this time with a specific mission in mind.

One of my goals for 2026 is to figure out exactly how useful agentic systems can be for cheminformatics. What tools do we need to give to AI agents so they can work with molecules? Can agents help with applied research activities like benchmarking and building optimal virtual screening workflows?

I’ll be building custom tools, experimenting with different frameworks, and documenting what works (and what doesn’t). If you’re interested in the intersection of AI agents and chemistry, follow along.

Let’s see where this goes.

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Building An Agentic Cheminformatics Workflow Tool

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One of my goals for 2026 is to figure out exactly how useful agentic systems can be for cheminformatics and drug discovery. To get started I built chemscii to learn the basics of model context protocol (MCP) server and Claude Code tool development. However, the chemscii tool itself was a toy example. In this post we will start to explore building agentic tools that might be useful for answering real cheminformatics and drug discovery research questions.