+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Quantitative calculations of antibody--antigen binding: steroid--DB3 binding energies by the linear interaction energy method



Quantitative calculations of antibody--antigen binding: steroid--DB3 binding energies by the linear interaction energy method



Journal of Organic Chemistry 66(9): 3021-3026



Linear interaction energy/molecular dynamics calculations have been used to compute steroid/antibody binding energies. The absolute binding affinities of 10 steroids to antibody DB3 and of a hapten to catalytic antibody 1E9 are computed and compared to experiment. A detailed analysis of the molecular origins of the observed binding patterns is provided. The binding energy of an untested steroid is predicted.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 047148721

Download citation: RISBibTeXText

PMID: 11325266

DOI: 10.1021/jo001619m


Related references

The linear interaction energy method for predicting ligand binding free energies. Combinatorial Chemistry and High Throughput Screening 4(8): 613-626, 2001

Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method. Journal of Chemical Theory and Computation 5(2): 380-395, 2009

Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method. Journal of Chemical Information and Modeling 46(5): 1972-1983, 2006

What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?. Proteins 34(3): 395-402, 1999

Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity. Journal of Molecular Graphics and Modelling 27(8): 930-943, 2009

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. Journal of Computational Chemistry 33(29): 2340-2350, 2012

Relative energies of binding for antibody-carbohydrate-antigen complexes computed from free-energy simulations. Journal of the American Chemical Society 122(2): 331-338, 2000

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Engineering 5(3): 215-228, 1992

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations. Philosophical Transactions. Series A Mathematical Physical and Engineering Sciences 363(1833): 2037-2053, 2005

Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design. Current Pharmaceutical Design 19(26): 4674-4686, 2013

Comparison between antigen-antibody binding energies and interfacial free energies. Immunological Communications 6(4): 341-354, 1977

Examining methods for calculations of binding free energies LRA, LIE and PDLD/S-LRA calculations of ligands binding to proteins. Biophysical Journal 78(1 Part 2): 332A, 2000

In silico binding free energy predictability by using the linear interaction energy (LIE) method: bromobenzimidazole CK2 inhibitors as a case study. Journal of Chemical Information and Modeling 47(2): 572-582, 2007

Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method. Journal of Medicinal Chemistry 42(25): 5142-5152, 1999