A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

2021 ◽  
Vol 23 (10) ◽  
pp. 6252-6265
Author(s):  
Alexander Gheorghiu ◽  
Peter V. Coveney ◽  
Alya A. Arabi
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Proton Transfer ◽  
Molecular Mechanics ◽  
Electric Fields ◽  
Base Pair ◽  
Realistic Model ◽  
External Electric Fields ◽  
Classical Molecular Dynamics

A detailed investigation is reported of mutagenic guanine–cytosine tautomerization in a realistic model of DNA bathed in intense electric fields using a combination of classical molecular dynamics and quantum mechanics/molecular mechanics methods.

The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†

2012 ◽  
Vol 34 (9) ◽  
pp. 750-756 ◽  
Author(s):  
Marcin Nowosielski ◽  
Marcin Hoffmann ◽  
Aneta Kuron ◽  
Malgorzata Korycka-Machala ◽  
Jaroslaw Dziadek
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics
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