Dengue Docking: The NS2B/NS3 Protease Target Workflow

By BioDockify Computational Research Team · October 11, 2026 · Disease Applications

A complete dengue computational project: why NS2B/NS3 protease is the classic hard target, which PDB structures to use, preparing the two-chain cofactor complex, grid placement on the catalytic triad, reference inhibitors, and what honest dengue docking results look like.

Read the complete article with tables, code and references on BioDockify.

Key References

• Noble, C.G. et al. Conformational change in the dengue virus NS2B/NS3 protease. Structure 20, 1204-1215 (2012).
• Lim, S.P., Noble, C.G., Seh, C.C. et al. Ten years of dengue drug discovery. Antiviral Res. 98, 271-279 (2013).
• Yildiz, M., Ghosh, S., Bell, J.A., Sherman, W. & Hardy, J.A. Alanine scanning identifies dengue protease residues. FEBS J. 280, 1517-1533 (2013).
• Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000). DOI: 10.1093/nar/28.1.235

Scope & Limitations

Dengue protease's shallow, polar active site makes it a notoriously hard docking target - poor scores here are the rule, not a protocol failure Serotype differences among the four dengue serotypes affect pocket geometry; state which serotype you studied