Optimizing Ligand Charges for Maximum Binding Affinity. A Solvated Interaction Energy Approach

2001 ◽  
Vol 105 (4) ◽  
pp. 889-899 ◽  
Author(s):  
Traian Sulea ◽  
Enrico O. Purisima
Keyword(s):  
Interaction Energy ◽  
Binding Affinity ◽  
Energy Approach ◽  
Solvated Interaction Energy

scholarly journals Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

2014 ◽  
Vol 15 (1) ◽  
pp. 798-816 ◽  
Author(s):  
C. Ruben Vosmeer ◽  
René Pool ◽  
Mariël van Stee ◽  
Lovorka Perić-Hassler ◽  
Nico Vermeulen ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Binding Affinity ◽  
Energy Approach ◽  
Linear Interaction ◽  
Binding Affinity Prediction ◽  
Linear Interaction Energy ◽  
Affinity Prediction

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

2008 ◽  
Vol 379 (4) ◽  
pp. 787-802 ◽  
Author(s):  
Qizhi Cui ◽  
Traian Sulea ◽  
Joseph D. Schrag ◽  
Christine Munger ◽  
Ming-Ni Hung ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Interaction Energy ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Solvated Interaction Energy

Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space

2007 ◽  
Vol 47 (1) ◽  
pp. 122-133 ◽  
Author(s):  
Marwen Naïm ◽  
Sathesh Bhat ◽  
Kathryn N. Rankin ◽  
Sheldon Dennis ◽  
Shafinaz F. Chowdhury ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Interaction Energy ◽  
Parameter Space ◽  
Binding Affinities ◽  
Solvated Interaction Energy

scholarly journals Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

2021 ◽  
Author(s):  
Prashant Kumar ◽  
Paulina Dominiak
Keyword(s):  
Interaction Energy ◽  
Molecular Dynamic ◽  
Binding Affinity ◽  
Electrostatic Interaction ◽  
Electrostatic Interactions ◽  
Data Bank ◽  
Scoring Functions ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Hiv 1

<div> <div> <div> <p>Computational analysis of protein-ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse on the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions such as in docking programs, we could say that they all rely on equations that sum each type of protein-ligand interactions to model the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions contribute one of the most important part of total interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this paper, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and Darunavir) have been analysed using charge densities from a transferable aspherical-atom data bank. Moreover, we analyse the electrostatic interaction energy for an ensemble of structures using molecular dynamic simulation to highlight the main features related to the importance of this interaction for binding affinity. </p> </div> </div> </div>

scholarly journals Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

2021 ◽  
Author(s):  
Prashant Kumar ◽  
Paulina Dominiak
Keyword(s):  
Interaction Energy ◽  
Molecular Dynamic ◽  
Binding Affinity ◽  
Electrostatic Interaction ◽  
Electrostatic Interactions ◽  
Data Bank ◽  
Scoring Functions ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Hiv 1

<div> <div> <div> <p>Computational analysis of protein-ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse on the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions such as in docking programs, we could say that they all rely on equations that sum each type of protein-ligand interactions to model the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions contribute one of the most important part of total interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this paper, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and Darunavir) have been analysed using charge densities from a transferable aspherical-atom data bank. Moreover, we analyse the electrostatic interaction energy for an ensemble of structures using molecular dynamic simulation to highlight the main features related to the importance of this interaction for binding affinity. </p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document