SASA Analysis in Molecular Dynamics: Measuring Solvent Exposure

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

How to use Solvent Accessible Surface Area (SASA) analysis in MD simulations. Covers hydrophobic vs hydrophilic SASA, protein folding indicators, and binding pocket analysis.

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

Key References

• Shrake, A. & Rupley, J.A. Environment and exposure to solvent of protein atoms. J. Mol. Biol. 79, 351-371 (1973).
• Eisenhaber, F. et al. The double cubic lattice method: Efficient computation of a smoothed solvent-accessible surface area. J. Comput. Chem. 16, 273-284 (1995).

Scope & Limitations

SASA depends on probe radius Does not distinguish between water types Per-residue SASA can be noisy