Protein-Ligand Contact Analysis in Molecular Dynamics

By BioDockify Computational Research Team · August 9, 2026 · MD Analysis

How to analyze protein-ligand contacts during MD simulation. Covers hydrogen bonds, hydrophobic contacts, salt bridges, water-mediated contacts, pi-stacking, and residue-level interaction maps.

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

Key References

• Laskowski, R.A. & Swindells, M.B. LigPlot+: multiple ligand-protein interaction diagrams. J. Chem. Inf. Model. 51, 2778-2786 (2011).
• Baker, E.N. & Hubbard, R.E. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44, 97-179 (1984).
• Hubbard, R.E. & Haider, M.K. Hydrogen bonds in proteins. eLS (2010).

Scope & Limitations

Contact and H-bond definitions vary between tools Water-mediated contacts require special analysis Geometric criteria are approximate