cgenff

Three Nigella sativa alkaloids (indazoles nigellidine, nigellicine; isoquinoline nigellimine) vs S. aureus FtsZ (PDB 3VOA): ADMET screening; docking with Vina, AutoDock4, GNINA, DiffDock-L (redock RMSD 0.307 Å); 4I55 tubulin counter-screen; 100 ns MD; MM-GBSA −13.28 ± 0.97 kcal/mol (SD). Computational predictions only.

A reproducible, end-to-end computational pipeline that uses a machine-learning docking surrogate and receptor-aware fragment growing to design a new Nrf2-inhibitor candidate, followed by force-field parametrization, explicit-solvent energy minimization, and AI-assisted retrosynthetic assessment.

This repository contains files to prepare small molecules paramters using cgenff, gaff2 and opls.