+ 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

What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?



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



Recently a semiempirical method has been proposed by Aqvist et al. to calculate absolute and relative binding free energies.

Please choose payment method:






(PDF emailed within 1 workday: $29.90)

Accession: 011650738

Download citation: RISBibTeXText

PMID: 10024025


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

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

Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method. Journal of Medicinal Chemistry 47(4): 1018-1030, 2004

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

Molecular dynamics simulations of 2-amino-6-arylsulphonylbenzonitriles analogues as HIV inhibitors: interaction modes and binding free energies. Chemical Biology and Drug Design 76(6): 518-526, 2010

Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse-grained molecular dynamics simulations with a weighted histogram analysis method. Journal of Computational Chemistry 38(23): 2007-2019, 2017

Efficient nonequilibrium method for binding free energy calculations in molecular dynamics simulations. Journal of Chemical Theory and Computation 11(2): 423-435, 2015

Computations of standard binding free energies with molecular dynamics simulations. Journal of Physical Chemistry. B 113(8): 2234-2246, 2009

Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations. Langmuir 26(11): 8347-8351, 2010

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations. Protein Engineering 8(11): 1137-1144, 1995

Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations. Journal of Computational Chemistry 26(12): 1294-1305, 2005

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. Journal of Molecular Biology 297(5): 1145-1158, 2000

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

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

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