Build and cluster diverse 3D libraries

Cresset Discovery Services (CDS) worked with BioBlocks to analyze their fragment library to maximize coverage of 3D chemical space. As part of the project, we developed an innovative clustering method that made it possible to assess the 3D similarity across their virtual database of over 1.5 million fragments.

The goal of the project was to help BioBlocks build the maximum 3D diversity into a fragment library of manageable size from a starting pool of over a million compounds. Existing techniques would have required an infeasible amount of computing power, so CDS developed an entirely novel rapid clustering method especially for the project. The solution was still extremely computationally challenging, but we were able to use our expertise in distributing calculations to the cloud to deliver the results that BioBlocks needed on time and within budget.

“Working with Cresset has been a positive experience from start to finish,” said Warren Wade, VP of Chemistry at BioBlocks. “Because our fragments are designed to be new chemical matter, they challenged the limits of existing structural descriptions. Cresset worked closely with us to overcome these limits and produce a high value compound set”.

The final result was a 3D fragment library that contains a significant number of compounds with novel core structures that are now viable candidates for fragment screening. BioBlocks envisions this Comprehensive Fragment Library to be a drug discovery tool available only to collaborators who will be able to leverage this new chemical space for their lead discovery programs. Hits from the library are entry points to BioBlocks’ collaborative medicinal chemistry processes, developed to increase the probability of generating commercially viable leads.


3D Similarity-based clustering workflow
3D similarity-based clustering workflow

Read more about this project: Large scale compound clustering in 3D.

Contact Cresset Discovery Services to find out more about how we can help you design large scale libraries for your project.