Why we're building De Novo Chem

Welcome to the De Novo Chem blog! This is where we'll share technical deep-dives, product updates, and insights from the world of cheminformatics.

For our first post, we wanted to briefly explain the problem we're trying to solve with De Novo Chem: affordable access to chemical data and tools. At our most recent roles, we worked at a small organization that couldn't afford the standard enterprise solutions for chemical searching — Reaxys and SciFinder. If you've ever had and then lost access to these databases, you'll know the pain of trying to search the chemical literature without them.

Why free tools aren't enough

There are plenty of excellent free tools like Google Scholar or Google Patents that can help you find a specific scholarly documents fast... but that only really helps you if you already know what document you're looking for. Forget about using these tools to quickly find compounds with a specific substructure, or to find conditions for a reaction you're trying to run. It can even be difficult to just find references to a specific compound. The reference might be out there, but impossible to find because:

• The authors named the compound differently than you expected, so searching by name yields no results. Did they call it N-[4-Methyl-3-[[4-(3-pyridinyl)-2-pyrimidinyl]amino]benzoyl]-4-[(4-methyl-1-piperazinyl)methyl]benzenamine, or 4-methyl-N-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide, or any of the other countless "IUPAC-like" names this compound could have? (We dig into this nomenclature problem in our next post.)
• The authors named the compound, but that name is "Compound 3f", and the only way to know what that refers to is by looking at an image of the structure in the S.I.
• The free tools weren't designed with chemical searches in mind — no similarity search, no substructure search, no way to draw the structure, no searching for compounds by structural properties, just regular plain text search. Tools like PubChem and OPSIN help with parts of this workflow, but they don't solve the core problem of searching across the literature by structure.

What might've been a 1-minute search with Reaxys or SciFinder now turns into a multi-hour affair with the free tools. It's frustrating to know that the data you seek is out there, but the tools to find it are locked behind a paywall that you or your organization can't afford. We started De Novo Chem because we think that access to chemical data and tools shouldn't be out of reach for small organizations, independent researchers, or anyone who can't afford the steep subscription costs of enterprise solutions.

What we're building

That's why we're committed to:

• Providing tools with transparent and fair pricing for individuals and small teams
• Tools that don't require an institutional affiliation
• Open source contributions wherever possible

We're starting by launching Saguaro Chem, our web-based chemical reaction database that lets you search by structure, substructure, or similarity across peer-reviewed literature and patents — no institutional access required. This tool is still early, and you can expect it to improve and evolve as we continue to expand the coverage, explore the underlying data, and gather feedback from our users.

If you run into a problem, a frustration, or even just have a suggestion as an individual chemist or a chemist from a small organization, we'd love to hear from you. As we work on these problems we'll publish the process, lessons, and insights right here on this blog.