A new Model for the Free Energy of Solvation and its Application in Protein Ligand Scoring
Please always quote using this URN: urn:nbn:de:0297-zib-8265
- A new and time efficient model to evaluate the free energy of solvation has been developed. The solvation free energy is separated into an electrostatic term, a hydrogen bond term, and a rest-term, combining both entropic and van der Waals effects. The electrostatic contribution is evaluated with a simplified boundary element method using the partial charges of the MMFF94 force field. The number of hydrogen bonds and the solvent excluded surface area over the surface atoms are used in a linear model to estimate the non-electrostatic contribution. This model is applied to a set of 213 small and mostly organic molecules, yielding an rmsd of 0.87kcal/mol and a correlation with experimental data of r=0.951. The model is applied as a supplementary component of the free energy of binding to estimate binding constants of protein ligand complexes. The intermolecular interaction energy is evaluated by using the MMFF94 force field.
Author: | Timm Baumeister, Frank Cordes |
---|---|
Document Type: | ZIB-Report |
Tag: | free energy; scoring; solvation |
MSC-Classification: | 92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92-08 Computational methods |
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C40 Biochemistry, molecular biology | |
Date of first Publication: | 2004/12/20 |
Series (Serial Number): | ZIB-Report (04-51) |
ZIB-Reportnumber: | 04-51 |