Ligand solvation in molecular docking

Proteins. 1999 Jan 1;34(1):4-16. doi: 10.1002/(sici)1097-0134(19990101)34:1<4::aid-prot2>;2-6.


Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Aniline Compounds / chemistry
  • Binding Sites*
  • Computer Simulation
  • Databases, Factual
  • Indoles / chemistry
  • Kinetics
  • Ligands
  • Lysosomes / chemistry
  • Models, Molecular
  • Protein Binding*
  • Pteridines / chemistry
  • Tetrahydrofolate Dehydrogenase / chemistry
  • Thymidine Monophosphate / chemistry


  • 2,4-diaminopteridine
  • 4,4'-sulfonyl-bis(N-(5-indanylmethylene)aniline)
  • Aniline Compounds
  • Indoles
  • Ligands
  • Pteridines
  • Thymidine Monophosphate
  • indole
  • Tetrahydrofolate Dehydrogenase