Development of the bioinformatics repository BioBricks
BioBricks (Insilica) is an application that makes large bioinformatics databases programmatically accessible. Because of the potential usefulness of this tool for toxicological data acquisition and analysis, NICEATM began working in 2022 with Insilica to provide support and testing of the BioBricks platform. A specific goal was to develop a BioBrick to query the Protein Data Bank, a U.S. government resource that represents the largest database of 3D protein structures. The Protein Data Bank includes binding affinity data for many protein-ligand complexes, which is an important resource to anticipate chemical actions. These binding affinity data are a key resource for a subsequent NICEATM activity, development of a biological similarity metric wherein chemicals that share a large number of biological effects will be considered similar. This metric may be useful for evaluating chemical hazard molecular mechanisms. NICEATM is also supporting testing and expanding the BioBricks interface through activities such as development of a Python version. All databases integrated into BioBricks are fully and freely available; the code is open-source and available via a GitHub repository.