Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials

2009 ◽  
Vol 78 (1) ◽  
pp. 83-94 ◽  
Author(s):  
Agustí Emperador ◽  
Tim Meyer ◽  
Modesto Orozco
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Flexibility ◽  
Discrete Molecular Dynamics ◽  
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 Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

2017 ◽  
Vol 3 (7) ◽  
pp. e1700479 ◽  
Author(s):  
Nicholas I. Brodie ◽  
Konstantin I. Popov ◽  
Evgeniy V. Petrotchenko ◽  
Nikolay V. Dokholyan ◽  
Christoph H. Borchers
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Distance ◽  
Protein Structures ◽  
Cross Linking ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations

PROTEOMICS ◽  
2021 ◽  
pp. 2000298
Author(s):  
Jason J. Serpa ◽  
Konstantin I. Popov ◽  
Evgeniy V. Petrotchenko ◽  
Nikolay V. Dokholyan ◽  
Christoph H. Borchers
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Distance ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

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

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

2012 ◽  
Vol 8 (11) ◽  
pp. 4707-4718 ◽  
Author(s):  
Pedro Sfriso ◽  
Agusti Emperador ◽  
Laura Orellana ◽  
Adam Hospital ◽  
Josep Lluis Gelpí ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transition ◽  
Discrete Molecular Dynamics ◽  
Transition Pathways ◽  
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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