+ 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

The linear interaction energy method for predicting ligand binding free energies



The linear interaction energy method for predicting ligand binding free energies



Combinatorial Chemistry and High Throughput Screening 4(8): 613-626



An overview of the simplified linear interaction energy (LIE) method for calculation of ligand binding free energies is given. This method is based on force field estimations of the receptor-ligand interactions and thermal conformational sampling. A notable feature is that the binding energetics can be predicted by considering only the intermolecular interactions between the ligand and receptor. The approximations behind this approach are examined and different parametrizations of the model are discussed. In general, LIE type of methods appear particularly useful for computational drug lead optimization.

Please choose payment method:






(PDF emailed within 1 workday: $29.90)

Accession: 047674838

Download citation: RISBibTeXText

PMID: 11812258


Related references

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

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

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. Journal of Chemical Information and Modeling 51(9): 2047-2065, 2011

Quantitative calculations of antibody--antigen binding: steroid--DB3 binding energies by the linear interaction energy method. Journal of Organic Chemistry 66(9): 3021-3026, 2001

Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies. Journal of Chemical Theory and Computation 3(6): 2162-2175, 2007

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

A new method for predicting binding free energy between receptor and ligand. Proteins. 33(1): 62-73,. 1, 1998

Application of the linear interaction energy method (LIE) to estimate the binding free energy values of Escherichia coli wild-type and mutant arginine repressor C-terminal domain (ArgRc)-l-arginine and ArgRc-l-citrulline protein-ligand complexes. Journal of Molecular Graphics and Modelling 22(4): 249-262, 2004

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

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

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

Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology 371(4): 1118-1134, 2007

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

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. Journal of Computational Chemistry 37(17): 1589-1600, 2016

Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. Journal of Computer-Aided Molecular Design 33(1): 105-117, 2019