diffdock

Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"

Analysis toolkit for AlphaFold3 biomolecular complex predictions (Protein-DNA, Protein-RNA, Protein-Ligand). Parses PAE error matrices, SASA, and interface binding energies.

Run molecular AI models locally with one command: Boltz-2, RFD4-Proteina, BindCraft2, DiffDock-L, ProteinMPNN, OpenDDE. Protein structure prediction, binder design and docking on Apple Silicon, Linux/NVIDIA or your own Runpod GPU. Works with Claude Code and Codex.

Benchmarking DiffDock-Pocket on LP-HiQBind and PoseBusters: ~50% of poses within 2 Å, but under 7% physically valid. Full HTCondor training, inference and evaluation pipeline.

Lightweight AI drug virtual screening platform for biologic industry. Nearly 20 years of expertise in biopharma R&D, manufacturing, quality and regulatory affairs.

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.

Benchmarking NVIDIA BioNeMo & NIM (DiffDock) inference scaling vs local CPU compute for structure-based drug discovery.

STRAND: Structure Refinement of RNA-Protein Complexes via Diffusion

Blinded, scaffold-split benchmark of AI docking vs classical docking on M. tuberculosis InhA

Do structural priors help a co-folding model? PLIP constraints from crystals and DiffDock poses, fed to Boltz-2 and measured against an unconstrained baseline.

Docking by denoising: DiffDock-L candidate poses, their reverse-diffusion trajectories and physical checks, and a frozen pilot comparing four ways to select a pose. Interactive article.

Prospective virtual screening of vendor catalogues against carbonic anhydrase with Boltz-2, plus DiffDock/PLIP constraint re-ranking