About MolNexus

MolNexus brings together the most powerful tools for molecular docking and protein design in one unified platform. No more juggling multiple software installations, command-line tools, or file format conversions. Virtual screening, sequence design, and 3D visualization—all accessible from your browser, ready to use in seconds.

AutoDock Vina

Virtual screening and molecular docking to predict how small molecules bind to protein targets.

  • Interactive 3D docking box definition with 3Dmol.js
  • Batch processing of multiple ligands
  • Binding affinity prediction (kcal/mol)
  • 3D pose visualization and comparison
  • Export results to CSV and PDBQT
Supported formats: PDB, CIF/mmCIF, PDBQT (receptors) | SDF, MOL2, MOL, PDBQT (ligands)
Reference: Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461. DOI: 10.1002/jcc.21334
ProteinMPNN

Design protein sequences for given backbone structures. Generate sequences optimized to fold into your target conformation.

  • Select specific chains to design
  • Fix residue positions to preserve key amino acids
  • Generate multiple sequence variants
  • Adjustable sampling temperature
  • Export sequences to FASTA
Reference: Dauparas, J., et al. (2022). Robust deep learning-based protein sequence design using ProteinMPNN. Science, 378(6615), 49-56. DOI: 10.1126/science.add2187
LigandMPNN

Design protein sequences considering ligand context. Engineer binding proteins and enzymes that interact with specific small molecules.

  • Ligand-aware sequence design
  • Configurable ligand cutoff distance
  • Optional side-chain packing
  • Support for multiple ligands
  • Export sequences to FASTA
Reference: Dauparas, J., et al. (2025). Atomic context-conditioned protein sequence design using LigandMPNN. Nature Methods. DOI: 10.1038/s41592-025-02626-1