Protein flexibility: Multiple molecular dynamics simulations of insulin chain B

2006 ◽  
Vol 119 (2) ◽  
pp. 146-157 ◽  
Author(s):  
F.S. Legge ◽  
A. Budi ◽  
H. Treutlein ◽  
I. Yarovsky
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Flexibility ◽  
Dynamics Simulations

Protein flexibility using constraints from molecular dynamics simulations

2005 ◽  
Vol 2 (4) ◽  
pp. S137-S147 ◽  
Author(s):  
Tatyana Mamonova ◽  
Brandon Hespenheide ◽  
Rachel Straub ◽  
M F Thorpe ◽  
Maria Kurnikova
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Flexibility ◽  
Dynamics Simulations

scholarly journals Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

2021 ◽  
Vol 8 ◽  
Author(s):  
Paulo C. T. Souza ◽  
Vittorio Limongelli ◽  
Sangwook Wu ◽  
Siewert J. Marrink ◽  
Luca Monticelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Throughput ◽  
Protein Flexibility ◽  
Md Simulations ◽  
Protein Docking ◽  
Rational Drug Design ◽  
Coarse Grained ◽  
Scoring Functions ◽  
Dynamics Simulations

Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.

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