Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method

RSC Advances ◽  
2015 ◽  
Vol 5 (129) ◽  
pp. 107020-107030 ◽  
Author(s):  
Jinfeng Liu ◽  
Xianwei Wang ◽  
John Z. H. Zhang ◽  
Xiao He
Keyword(s):  
Ligand Binding ◽  
Quantum Mechanical ◽  
Binding Affinities ◽  
Mechanical Method ◽  
Reliable Prediction ◽  
Quantum Mechanical Method

An efficient fragment-based quantum mechanical method has been successfully applied for reliable prediction of protein–ligand binding affinities.

Computational methods for calculation of protein-ligand binding affinities in structure-based drug design

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Zbigniew Dutkiewicz
Keyword(s):  
Drug Design ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Development Project ◽  
Quantum Mechanical ◽  
Prediction Methods ◽  
Binding Affinities ◽  
Structure Based Drug Design ◽  
Quantum Mechanical Description ◽  
Optimization Stage

AbstractDrug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.

scholarly journals On the electromagnetic fields due to variable electric charges and the intensities of spectrum lines according to the quantum theory

1935 ◽  
Vol 150 (870) ◽  
pp. 416-421 ◽  
Keyword(s):  
Quantum Theory ◽  
Wave Functions ◽  
Spectral Lines ◽  
Quantum Mechanical ◽  
Final States ◽  
Electric Moment ◽  
Mechanical Method ◽  
Quantum Mechanical Method ◽  
Consistent Method ◽  
Time Average

In a recent paper Schott has criticized the quantum mechanical method of finding the intensities of spectral lines, and in particular the assumption that the intensity may be derived by treating the atom as a dipole, radiating classically. The electric moment of this dipole is taken as p = e -2 πivt ∫ Ψ* f rΨ i d τ + Conjugate complex, (1A) where Ψ i and Ψ f are the wave functions of the initial and final states of the atom respectively, and in the Quantum Theory the usual assumption is that the energy radiated per unit time is given by R = 2 |p¨ ¯ | 2 /3 c 2 , (1B) where p¨ ¯ is the time average of p¨. A more consistent method is suggested in which the electric density ρ and the current j, corresponding to the transition, are found, and the electromagnetic field due to these two is examined.

A quantum mechanical approach to ligand binding — Calculation of ligand–protein binding affinities for stromelysin-1 (MMP-3) inhibitors

2009 ◽  
Vol 87 (10) ◽  
pp. 1480-1484 ◽  
Author(s):  
Jian Li ◽  
Charles. H. Reynolds
Keyword(s):  
Ligand Binding ◽  
Metal Ion ◽  
Protein Complexes ◽  
Field Method ◽  
Binding Energies ◽  
Quantum Mechanical ◽  
Binding Affinities ◽  
Bond Forming ◽  
Proton Charge ◽  
Quantum Mechanical Approach

Linear-scaling quantum mechanical method was applied to calculate binding affinities of six stromelysin-1 (MMP-3) inhibitors with two different zinc binding groups (ZBGs). The entire protein and ligand–protein complexes were calculated using PM5 Hamiltonian, which enables the treatment of metal ion coordination, bond forming/breaking, and proton/charge transfers associated with the ligand binding process by the self-consistent field method. The calculated binding energies reproduce the binding-affinity trend observed experimentally.

Nonresonant Diffusion of Particles in Stochastic Fields

1971 ◽  
Vol 26 (2) ◽  
pp. 181-185 ◽  
Author(s):  
D. Biskamp ◽  
D. Pfirsch
Keyword(s):  
Electromagnetic Fields ◽  
Planck Equation ◽  
Resonant Scattering ◽  
Quantum Mechanical ◽  
Weak Turbulence ◽  
Mechanical Method ◽  
Stochastic Fields ◽  
Fokker Planck Equation ◽  
Simple Quantum ◽  
Quantum Mechanical Method

AbstractA Fokker-Planck equation for the non-resonant scattering of particles by general weakly turbulent electromagnetic fields is derived using a simple quantum-mechanical method. The equation is compared with the corresponding weak turbulence equation as given e. g. in Kadomtsev's book and two applications are discussed.

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