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Theoretical and Computational Chemistry

Working Paper

PySurf - A Framework for Database Accelerated Direct Dynamics

Shirin Faraji, Johannes Ehrmaier, Maximilian Menger

Version 1 posted 28 October 2020

272

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Theoretical and Computational Chemistry

Working Paper

Membrane Permeation of Psychedelic Compounds

Vito Federico Palmisano, Claudio Agnorelli, Andrea Fagiolini, David Erritzoe, David Nutt, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 31 October 2023

314

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Theoretical and Computational Chemistry

Working Paper

Effect of Stacking Interactions on Charge Transfer States in Photoswitches Interacting with Ion Channels

Vito Federico Palmisano, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 14 October 2022

186

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Biological and Medicinal Chemistry

Review

Light-Induced Control of Voltage Gated Ion Channels

Vito F. Palmisano, Nuria Anguita-Ortiz, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 07 April 2022

578

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Theoretical and Computational Chemistry

Working Paper

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

Vale Cofer-Shabica, Maximilian Menger, Qi Ou, Yihan Shao, Joseph Subotnik, Shirin Faraji

Version 1 posted 02 March 2022

208

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1

Citations

Theoretical and Computational Chemistry

Working Paper

QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

Bella L. Grigorenko, Igor V. Polyakov, Maria G. Khrenova, Goran Giudetti, Shirin Faraji, Anna I. Krylov, Alexander V. Nemukhin

Version 2 posted 02 March 2023

793

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Theoretical and Computational Chemistry

Working Paper

HOAX: A Hyperparameter Optimization Algorithm Explorer for Neural Networks

Albert Thie, Maximillian F.S.J. Menger, Shirin Faraji

Version 1 posted 02 February 2023

156

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Theoretical and Computational Chemistry

Working Paper

Characterization of the Binding Poses of Classical and Photoswitchable Psychedelics Interacting with 5-HT2AR

Vito Palmisano, Claudio Agnorelli, David Erritzoe, Andrea Fagiolini, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 08 February 2023

489

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Theoretical and Computational Chemistry

Working Paper

Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4

Vito F. Palmisano, Carlos Gómez-Rodellar, Hannah Pollak, Gustavo Cárdenas, Ben Corry, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 02 December 2020

500

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Theoretical and Computational Chemistry

Working Paper

How Reproducible are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

Goran Giudetti, Igor Polyakov, Bella L. Grigorenko, Shirin Faraji, Alexander V. Nemukhin, Anna I. Krylov

Version 1 posted 18 March 2022

556

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Refine Search

13 results in Shirin Faraji in Authors: Shirin Faraji

PySurf - A Framework for Database Accelerated Direct Dynamics

Membrane Permeation of Psychedelic Compounds

Effect of Stacking Interactions on Charge Transfer States in Photoswitches Interacting with Ion Channels

Light-Induced Control of Voltage Gated Ion Channels

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

HOAX: A Hyperparameter Optimization Algorithm Explorer for Neural Networks

Characterization of the Binding Poses of Classical and Photoswitchable Psychedelics Interacting with 5-HT2AR

Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4

How Reproducible are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

13 results in Authors: Shirin Faraji