Conformational analysis of dolastatin 10 and dolastatin 15 by molecular mechanics and molecular dynamics

1995 ◽  
Author(s):  
P. Fantucci ◽  
T. Marino ◽  
N. Russo ◽  
A. M. Villa
Keyword(s):  
Molecular Dynamics ◽  
Conformational Analysis ◽  
Molecular Mechanics ◽  
Dolastatin 10

scholarly journals Conformational Analysis in 18-Membered Macrolactones Based on Molecular Modeling

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Salah Belaidi ◽  
Dalal Harkati
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Conformational Analysis ◽  
Molecular Mechanics ◽  
Conformational Flexibility ◽  
Molecular Mechanics Calculations

Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1% in presence of Fe(CO)3.

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.

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