Binding affinity prediction with different force fields: examination of the linear interaction energy method

M Almlöf, BØO Brandsdal… - Journal of computational …, 2004 - Wiley Online Library
… Another approach that has received considerable attention in the last years is the linear
interaction energy (LIE) method.9 This method is also based on conformational sampling by MD …

Spectra and binding energy predictions of chiral interactions for

A Nogga, P Navrátil, BR Barrett, JP Vary - Physical Review C, 2006 - APS
… In this article, we use the NCSM to predict spectra and binding energies for 7Li. These results
will be presented along with calculations for the s-shell states for 3H and 4He, which were …

Prediction of the binding energy for small molecules, peptides and proteins

M Schapira, M Totrov, R Abagyan - Journal of Molecular …, 1999 - Wiley Online Library
based on the physical contributions to the interaction, and should therefore be more universal
and transferable than knowledge-based … evaluating the electrostatic free energy of just one …

Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy …

MMH Van Lipzig, AM Ter Laak… - Journal of Medicinal …, 2004 - ACS Publications
… Therefore, the fact that the orientation with the best interaction energy, predicted by our
model for DES, E2, and THC, matches those found in the crystal structures of ERα LBD …

Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 …

J Carlsson, L Boukharta, J Åqvist - Journal of medicinal chemistry, 2008 - ACS Publications
… The only term representing polar interactions in this scoring function is a simple hydrogen …
In conclusion, the standard parametrization of eq 1 can predict the binding free energies of the …

Accurate prediction of noncovalent interaction energies with the effective fragment potential method: Comparison of energy components to symmetry-adapted …

JC Flick, D Kosenkov, EG Hohenstein… - Journal of chemical …, 2012 - ACS Publications
… The complete list of the EFP interaction energies for the S22 … Because the average interaction
energies of HB, dispersion-… value of the average interaction energies that provides an easy …

Assessing protein structures with a non-local atomic interaction energy

F Melo, E Feytmans - Journal of molecular biology, 1998 - Elsevier
… approach, based on the energy of non-local interactions, … prediction. The correct conformation
of a loop may have a high local interaction energy, and a technique based on local energy

A road map for the calculation of molecular binding energies

TH Dunning - The Journal of Physical Chemistry A, 2000 - ACS Publications
interaction energies is unambiguous. We will not discuss configuration interaction methods
… electron) CCSD(T) method predicts the bond energies to an accuracy of better than 1 kcal/…

Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies. Successes and failures

P Hobza, R Zahradnik - Chemical Reviews, 1988 - ACS Publications
… Strong interactions between protons and neu-trons result in the formation ofatomic nuclei.
Much weaker interactions between … Weak interactions have been traditionally associated with …

Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction

T Selzer, G Schreiber - Journal of molecular biology, 1999 - Elsevier
… Thus by calculating the contribution of a mutation to the electrostatic energy of interaction,
we can predict the degree to which this change will increase or decrease the rate of …