Open-source QM/MD toolkits for Computer-Aided Drug Design (CADD): interaction fingerprint analysis, trajectory mining, and molecular visualization.
Consensus-based visualisation of protein–protein interactions from MD trajectories
PLIF-based Interaction-fingerprint rescoring of AutoDock Vina poses for early enrichment (DUD-E CDK2)
Schrodinger-style 2D protein-ligand interaction diagrams from GROMACS trajectories: H-bond, pi, halogen, water bridge, ionic and metal coordination, with binding-site mode.
Automated pocket-guided molecular docking and protein–ligand interaction analysis pipeline using AutoDock Vina, P2Rank, Meeko, and ProLIF.
One-command GROMACS MD (laptop or SLURM GPU) for protein-ligand and apo systems, plus ligand RMSF, PCA/FEL and PCA+protein movie tools.
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