ProtoBuild™ is a de novo design application developed as part of the ProtoDiscovery™ platform. The application enables the generation of novel structures from a predefined palette of molecular fragments against a template which may be a derived from a protein structure or known active ligands. The program is extremely feature rich and provides many workflows to solve a range of drug design paradigms. Important application features include:

  • ProtoScore™ affinity prediction
  • Pharmacophore/SMARTS template definitions
  • Protein flexibility
  • Fragment connection data for improved synthetic feasibility
  • Structure-based and ligand-based design protocols
  • Mixed growing and linking modes
  • Infinite run modes
  • Virtual ligand concept
ProtoBuild frgament growing

ProtoBuild™ has been validated by use in a number of different partner-driven projects (see case studies). Recently ProtoBuild™ has been used to construct a number of novel molecules for different GPCR targets which, after synthesis, have been shown to bind to the relevant GPCR in in vitro assays.

The directed GPCR design approach has proved to be rapid and cost effective and may be driven by the chemistry knowledge of the our partner company by associating specific fragment rules.


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