scholarly journals Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

2015 ◽  
Vol 11 (3) ◽  
pp. 1337-1346 ◽  
Author(s):  
Steffen Lindert ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
High Precision ◽  
Structure Prediction ◽  
Structure Refinement ◽  
Protein Structure Refinement

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

2016 ◽  
Vol 84 (9) ◽  
pp. 1312-1320 ◽  
Author(s):  
Edoardo Sarti ◽  
Ivan Gladich ◽  
Stefano Zamuner ◽  
Bruno E. Correia ◽  
Alessandro Laio
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction

scholarly journals Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement

2001 ◽  
Vol 45 (S5) ◽  
pp. 149-156 ◽  
Author(s):  
Jeffrey Skolnick ◽  
Andrzej Kolinski ◽  
Daisuke Kihara ◽  
Marcos Betancourt ◽  
Piotr Rotkiewicz ◽  
...  
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Structure Refinement

scholarly journals Experimental accuracy in protein structure refinement via molecular dynamics simulations

2018 ◽  
Vol 115 (52) ◽  
pp. 13276-13281 ◽  
Author(s):  
Lim Heo ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Structure Prediction ◽  
Structure Refinement ◽  
Energy Landscape ◽  
Md Simulations ◽  
Homology Model ◽  
Experimental Accuracy ◽  
Markov State Modeling ◽  
Homology Models

Refinement is the last step in protein structure prediction pipelines to convert approximate homology models to experimental accuracy. Protocols based on molecular dynamics (MD) simulations have shown promise, but current methods are limited to moderate levels of consistent refinement. To explore the energy landscape between homology models and native structures and analyze the challenges of MD-based refinement, eight test cases were studied via extensive simulations followed by Markov state modeling. In all cases, native states were found very close to the experimental structures and at the lowest free energies, but refinement was hindered by a rough energy landscape. Transitions from the homology model to the native states require the crossing of significant kinetic barriers on at least microsecond time scales. A significant energetic driving force toward the native state was lacking until its immediate vicinity, and there was significant sampling of off-pathway states competing for productive refinement. The role of recent force field improvements is discussed and transition paths are analyzed in detail to inform which key transitions have to be overcome to achieve successful refinement.

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