Dimorphite-DL

pH-aware ligand protonation tool used before docking when charge state is part of the modeling question.

Why It Matters

Dimorphite-DL assigns likely protonation states before ligand conversion. That matters for STRC docking because the modeling question often depends on whether a head group is neutral, mono-anionic, or di-anionic at physiological pH.

Local Pattern

Use Dimorphite-DL before Meeko when preparing ligand libraries for Vina. Then verify that the generated state matches the intended chemistry class. This prevents a preparation pipeline from silently testing a different molecule than the one named in the experiment.

Connections

• [applies] Vina Ligand Prep — Gasteiger Zero-Anion Artifact and Dimorphite-Meeko Fix
• [see-also] Meeko
• [part-of] Tools