Receptor–Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method

2020 ◽  
Vol 16 (10) ◽  
pp. 6645-6655
Author(s):  
Hao Liu ◽  
Jianpeng Deng ◽  
Zhou Luo ◽  
Yawei Lin ◽  
Kenneth M. Merz ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Sampling Method ◽  
Monte Carlo Sampling ◽  
Free Energies ◽  
Receptor Ligand ◽  
Binding Free Energies

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

Biochemistry ◽  
1994 ◽  
Vol 33 (47) ◽  
pp. 13977-13988 ◽  
Author(s):  
Sandor Vajda ◽  
Zhiping Wheng ◽  
Rakefet Rosenfeld ◽  
Charles DeLisi
Keyword(s):  
Ligand Binding ◽  
Conformational Flexibility ◽  
Free Energies ◽  
Receptor Ligand ◽  
Binding Free Energies

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

scholarly journals Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

2021 ◽  
Author(s):  
Yuriy Khalak ◽  
Gary Tresdern ◽  
Matteo Aldeghi ◽  
Hannah Magdalena Baumann ◽  
David L. Mobley ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Drug Design ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains...

scholarly journals An integrated inverse adaptive neural fuzzy system with Monte-Carlo sampling method for operational risk management

2018 ◽  
Vol 98 ◽  
pp. 11-26 ◽  
Author(s):  
Alejandro Peña ◽  
Isis Bonet ◽  
Christian Lochmuller ◽  
Francisco Chiclana ◽  
Mario Góngora
Keyword(s):  
Risk Management ◽  
Monte Carlo ◽  
Fuzzy System ◽  
Sampling Method ◽  
Operational Risk ◽  
Monte Carlo Sampling ◽  
Operational Risk Management ◽  
Neural Fuzzy

Modeling and implementation of spin diode based on two dimensional materials using Monte Carlo sampling method

Circuit World ◽  
2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Swapnali Makdey ◽  
Rajendra Patrikar ◽  
Mohammad Farukh Hashmi
Keyword(s):  
Magnetic Field ◽  
Monte Carlo ◽  
Density Functional ◽  
Sampling Method ◽  
Spin Current ◽  
Electrical Current ◽  
Monte Carlo Sampling ◽  
Equilibrium Density ◽  
Content Type ◽  
Spin Diode

Purpose A “spin-diode” is the spintronics equivalent of an electrical diode: applying an external magnetic field greater than the limit of spin-diode BT flips the spin-diode between an isolating state and a conducting state [1]. While conventional electrical diodes are two-terminal devices with electrical current between the two terminals modulated by an electrical field, these two-terminal magneto resistive devices can generally be referred to as “spin-diodes” in which a magnetic field modulates the electrical current between the two terminals. Design/methodology/approach Current modulation and rectification are an important subject of electronics as well as spintronics spin diode is two-terminal magnetoresistive devices in which change in resistance in response to an applied magnetic field; this magnetoresistance occurs due to a variety of phenomena and with varying magnitudes and directions. Findings In this paper, an efficient rectifying spin diode is introduced. The resulting spin diode is formed from graphene gallium and indium quantum dots and antimony-doped molybdenum disulfide. Converting an alternating bias voltage to direct current is the main achievement of this model device with an additional profit of rectified spin-current. The non-equilibrium density functional theory with a Monte Carlo sampling method is used to evaluate the flow of electrons and rectification ratio of the system. Originality/value The results indicate that spin diode displaying both spin-current and charge-current rectification should be possible and may find practical application in nanoscale devices that combine logic and memory functions.

Capacity Expansion Problem by Monte Carlo Sampling Method

2009 ◽  
Vol 13 (6) ◽  
pp. 697-703
Author(s):  
Takayuki Shiina ◽  
Keyword(s):  
Monte Carlo ◽  
Variance Reduction ◽  
Sampling Method ◽  
Sampling Technique ◽  
Capacity Expansion ◽  
Monte Carlo Sampling ◽  
Previous Approach ◽  
Importance Sampling Technique ◽  
Stochastic Vector ◽  
Additive Form

We consider the stochastic programming problem with recourse in which the expectation of the recourse function requires a large number of function evaluations, and its application to the capacity expansion problem. We propose an algorithm which combines an L-shaped method and a Monte Carlo method. The importance sampling technique is applied to obtain variance reduction. In the previous approach, the recourse function is approximated as an additive form in which the function is separable in the components of the stochastic vector. In our approach, the approximate additive form of the recourse function is perturbed to define the new density function. Numerical results for the capacity expansion problem are presented.

Sign in / Sign up

Export Citation Format

Share Document