Solvated interaction energy (SIE) for scoring protein− ligand binding affinities. 1. Exploring the parameter space
… of parameter space. Aside from coefficients for the van der Waals interaction energy and
buried … of the electrostatic and nonelectrostatic solvation parameters, in conjunction with the …
buried … of the electrostatic and nonelectrostatic solvation parameters, in conjunction with the …
Interaction energy in geometrostatics
DR Brill, RW Lindquist - Physical Review, 1963 - APS
… description of particles by means of topological features of empty space-time is applied
here … and electrostatic interaction energies. It is shown that the interaction energy is always …
here … and electrostatic interaction energies. It is shown that the interaction energy is always …
Space-time description of the hadron interaction at high energies
VN Gribov - arXiv preprint hep-ph/0006158, 2000 - arxiv.org
… In the impact parameter space this propagator has the form (22). Let us discuss the physical
meaning of σ0 in more detail. For this purpose, let us calculate the zero angle scattering …
meaning of σ0 in more detail. For this purpose, let us calculate the zero angle scattering …
Making optimal use of empirical energy functions: force‐field parameterization in crystal space
E Krieger, T Darden, SB Nabuurs… - Proteins: Structure …, 2004 - Wiley Online Library
… parameters were iteratively adjusted so that the damage done to the structures was minimal.
Starting with initial parameters … Another Model Building and Energy Refinement force field), …
Starting with initial parameters … Another Model Building and Energy Refinement force field), …
Constraining the symmetry parameters of the nuclear interaction
JM Lattimer, Y Lim - The Astrophysical Journal, 2013 - iopscience.iop.org
… does not further limit parameter space and is therefore not displayed in Figure 2 for clarity.
Both limits have been established from specific types of nuclear interaction models, and may …
Both limits have been established from specific types of nuclear interaction models, and may …
Effects of the interaction between dark energy and dark matter on cosmological parameters
… By using two parameterizations for the EoS of DE ωI,ωII, we obtain the parameter space
for different couplings, respectively, and we will show our results in the following sections. For …
for different couplings, respectively, and we will show our results in the following sections. For …
[HTML][HTML] Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning
… In the following, we present the different terms in our interaction energy and how they rely …
), where π-stacking interactions dominate the interaction energy. The discrepancies likely arise …
), where π-stacking interactions dominate the interaction energy. The discrepancies likely arise …
Recent developments in linear interaction energy based binding free energy calculations
EA Rifai, M Van Dijk, DP Geerke - Frontiers in Molecular Biosciences, 2020 - frontiersin.org
… domain (AD) definition to provide a measure of confidence for predictions for arbitrary query
compounds within a reference frame defined by a collective chemical and interaction space. …
compounds within a reference frame defined by a collective chemical and interaction space. …
Assessing protein structures with a non-local atomic interaction energy
F Melo, E Feytmans - Journal of molecular biology, 1998 - Elsevier
… a high local interaction energy, and a technique based on local energy minimization would
… -range interaction energies between atoms, not covalently restricted to converge in space, …
… -range interaction energies between atoms, not covalently restricted to converge in space, …
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
A systematic study of the linear interaction energy (LIE) method and the possible dependence
of its parameterization on the force field and system (receptor binding site) is reported. We …
of its parameterization on the force field and system (receptor binding site) is reported. We …
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- linear interaction energy method
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- interaction energy protein ligand binding affinities