Bennett acceptance ratio method to calculate the binding free energy of BACE1 inhibitors: Theoretical model and design of new ligands of the enzyme

2019 ◽  
Vol 93 (6) ◽  
pp. 1117-1128 ◽  
Author(s):  
Margarita Gutiérrez ◽  
Gabriel A. Vallejos ◽  
Magdalena P. Cortés ◽  
Carlos Bustos
Keyword(s):  
Free Energy ◽  
Theoretical Model ◽  
Binding Free Energy ◽  
Ratio Method ◽  
Acceptance Ratio ◽  
Bennett Acceptance Ratio

scholarly journals A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.

2000 ◽  
Vol 47 (1) ◽  
pp. 1-9 ◽  
Author(s):  
W R Rudnicki ◽  
M Kurzepa ◽  
T Szczepanik ◽  
W Priebe ◽  
B Lesyng
Keyword(s):  
Free Energy ◽  
Theoretical Model ◽  
Density Functional ◽  
Binding Free Energy ◽  
Binding Energies ◽  
Free Energies ◽  
Anthracycline Antibiotics ◽  
Free Energy Of Binding ◽  
Derivatives Of ◽  
Binding Free Energies

A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.

scholarly journals Study of the effectiveness of various cannabinoid receptor 1 (CB1) agonists using molecular docking and molecular dynamics modeling

2020 ◽  
Vol 8 (1) ◽  
pp. 76-87
Author(s):  
Volodymyr Tkachenko ◽  
Vladimir Farafonov ◽  
Viktor Tokarev ◽  
Irina Tkachenko
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Cannabinoid Receptor ◽  
Binding Free Energy ◽  
Energy Estimates ◽  
Binding Modes ◽  
Dynamics Modeling ◽  
Acceptance Ratio ◽  
Molecular Dynamics Modeling ◽  
Poisson Boltzmann

The binding of a series of small organic molecules, acting as agonists of the cannabinoid receptor CB1, was investigated by means of three methods of computational chemistry. Binding modes were predicted by means of molecular docking, and binding free energy was estimated via docking, molecular-mechanics Poisson-Boltzmann surface area method, and multistate Bennett acceptance ratio. No evident correlation was observed for the molecules between the experimental characteristics of affinity and three computed binding free energy estimates. The reasons for the discrepancy were discussed.

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

2020 ◽  
Author(s):  
Christina Schindler ◽  
Hannah Baumann ◽  
Andreas Blum ◽  
Dietrich Böse ◽  
Hans-Peter Buchstaller ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Large Scale ◽  
Active Drug ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculation ◽  
Large Scale Assessment ◽  
New Public ◽  
Binding Free Energy Calculations

Here we present an evaluation of the binding affinity prediction accuracy of the free energy calculation method FEP+ on internal active drug discovery projects and on a large new public benchmark set.<br>

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