Starting structure-based design with sample compounds

Structure-based drug design starts with a compound positioned on the surface of a protein. Often, the crystal ligand in a PDB structure provides the natural starting point. But what if there is no ligand? This question took on increased urgency as the Boltzmann Maps team prepared fragment simulations on COVID-19 structures; many of the initial entries in the PDB did not have ligands. In response to this, Boltzmann Maps now provides Sample Compounds. We docked 20K+ small molecules from our libraries against hotspots on each structure and selected a handful to show in BMaps. The resulting compounds are generally commercially available, chemically diverse, and are reasonable starting points for structure-based design. They can then be used to explore new designs, using BMaps’ energy analysis and fragment data.

Sample Compounds are available for almost all of the SARS-CoV-2 structures in Boltzmann Maps. More are coming!

View a COVID-19 structure with sample compounds now >>. Or, log in to start exploring your own structure-based design modifications.

Continue reading Starting structure-based design with sample compounds