Benjamin J. Shields, Ph.D.

Benjamin J. Shields, Ph.D.

Chemist & Machine Learning Engineer

Hello World!

less than 1 minute read

Published:

My site basics are finished! Later I will add some posts on things I am working on.

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A Minimal Basis for Chemical Structure Comprehension and Editing

20 minute read

Published:

The ability to understand, reason about, and modify chemical structure is central to medicinal chemistry and structure-based drug discovery. Accordingly, chemical structure comprehension is a critical component for an agentic LLM system for small-molecule design. In this post we will explore chemical structure comprehension by developing a tree-based data structure and tools for agents to work with 2D and 3D chemical structures. Then we will test the framework against baseline LLM text editing and generalist LLM with bash tool calling.

Building An Agentic Cheminformatics Workflow Tool

14 minute read

Published:

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.