In silico software development
SATELLiTES is an open-source software designed to facilitate chemical space exploration and aid in the discovery of new hit compounds, starting from a specific two-reagents or three-components chemical reaction encoded in SMARTS format and a list of commercially available or ready-to-use compatible synthons. SATELLiTES is based on the hierarchical combinatorial approaches of synthon-based drug discovery, that can enable the fast exploration of ultra-large chemical libraries.
You can use SATELLiTES in two different ways:
- By using the graphical interface, downloadable from the Python Package Index (https://pypi.org/project/SATELLiTES-SBDD/)
- By using the KNIME extension, downloadable from the extension manager (https://github.com/cbedart/SATELLiTES)
As long as the structural study of molecular mechanisms requires multiple molecular dynamics reflecting contrasted bioactive states, the subsequent analysis of molecular interaction networks remains a bottleneck to be fairly treated and requires a user-friendly 3D view of key interactions.
Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python tool developed to:
- Quickly solve key interactions able to distinguish two protein states, either from two sets of molecular dynamics simulations or from two crystallographic structures, and
- Render a user-friendly 3D view of these key interactions through a plugin of UCSF Chimera, one of the most popular open-source viewing software for biomolecular systems.
SINAPs is freely available at https://github.com/ParImmune/SINAPs