scholarly journals Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure

2016 ◽  
Vol 35 (8-9) ◽  
pp. 449-459 ◽  
Author(s):  
Francesco Antonio Greco ◽  
Answald Bournique ◽  
Alice Coletti ◽  
Chiara Custodi ◽  
Daniela Dolciami ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Docking Studies ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

scholarly journals Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 118
Author(s):  
Siao Chen ◽  
Yi He ◽  
Yajiao Geng ◽  
Zhi Wang ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Md Simulations ◽  
Docking Studies ◽  
Molecular Dynamic Simulations ◽  
Terminal Protein ◽  
Dynamic Simulations ◽  
Binding Effect ◽  
Computational Alanine Scanning ◽  
Α Helix ◽  
Effect Of Inhibitors

Bromodomain and extra-terminal domain (BET) subfamily is the most studied subfamily of bromodomain-containing proteins (BCPs) family which can modulate acetylation signal transduction and produce diverse physiological functions. Thus, the BET family can be treated as an alternative strategy for targeting androgen-receptor (AR)-driven cancers. In order to explore the effect of inhibitors binding to BRD4 (the most studied member of BET family), four 150 ns molecular dynamic simulations were performed (free BRD4, Cpd4-BRD4, Cpd9-BRD4 and Cpd19-BRD4). Docking studies showed that Cpd9 and Cpd19 were located at the active pocket, as well as Cpd4. Molecular dynamics (MD) simulations indicated that only Cpd19 binding to BRD4 can induce residue Trp81-Ala89 partly become α-helix during MD simulations. MM-GBSA calculations suggested that Cpd19 had the best binding effect with BRD4 followed by Cpd4 and Cpd9. Computational alanine scanning results indicated that mutations in Phe83 made the greatest effects in Cpd9-BRD4 and Cpd19-BRD4 complexes, showing that Phe83 may play crucial roles in Cpd9 and Cpd19 binding to BRD4. Our results can provide some useful clues for further BCPs family search.

Molecular dynamic simulations of Co(III) and Ru(II) polypyridyl complexes and docking studies with dsDNA

2013 ◽  
Vol 22 (11) ◽  
pp. 5557-5565 ◽  
Author(s):  
Navaneetha Nambigari ◽  
Ramasree Dulapalli ◽  
Kiran Kumar Mustyala ◽  
Vasavi Malkhed ◽  
Uma Vuruputuri ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Docking Studies ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Polypyridyl Complexes

scholarly journals Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers

2021 ◽  
Vol 14 (7) ◽  
pp. 645
Author(s):  
Shaymaa A. Abd-algaleel ◽  
Hend M. Abdel-Bar ◽  
Abdelkader A. Metwally ◽  
Rania M. Hathout
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Molecular Dynamic ◽  
Docking Studies ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Polymeric Nanocarriers ◽  
Modeling And Prediction ◽  
Wet Lab ◽  
Key Aspects

This review describes different trials to model and predict drug payload in lipid and polymeric nanocarriers. It traces the evolution of the field from the earliest attempts when numerous solubility and Flory-Huggins models were applied, to the emergence of molecular dynamic simulations and docking studies, until the exciting practically successful era of artificial intelligence and machine learning. Going through matching and poorly matching studies with the wet lab-dry lab results, many key aspects were reviewed and addressed in the form of sequential examples that highlighted both cases.

scholarly journals Ranking the Efficiency of Gas Hydrate Anti-agglomerants through Molecular Dynamic Simulations

2021 ◽  
Vol 125 (5) ◽  
pp. 1487-1502
Author(s):  
Stephan Mohr ◽  
Felix Hoevelmann ◽  
Jonathan Wylde ◽  
Natascha Schelero ◽  
Juan Sarria ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Gas Hydrate ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations
Sign in / Sign up

Export Citation Format

Share Document