DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such that the resulting extension is also highly complementary to the receptor.
LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.
POVME2 (POcket Volume MEasurer 2) scans a molecular-dynamics simulation and extracts druggable protein pockets with unique conformations. Virtual screens that leverage these conformations often identify novel active molecules.
FpocketWeb is a browser app for identifying pockets on protein surfaces where small-molecule ligands (e.g., drugs) might bind. It runs the fpocket executable entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.
BINANA analyzes docked ligand poses to identify molecular interactions that contribute to binding. Accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study.