Homology Modeling and Molecular Dynamics Simulation Combined with X-ray Solution Scattering Defining Protein Structures of Thromboxane and Prostacyclin Synthases

2017 ◽  
Vol 121 (50) ◽  
pp. 11229-11240 ◽  
Author(s):  
Hsiao-Ching Yang ◽  
Cheng-Han Yang ◽  
Ming-Yi Huang ◽  
Jyh-Feng Lu ◽  
Jinn-Shyan Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Protein Structures ◽  
Dynamics Simulation ◽  
X Ray

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

scholarly journals Homology modeling and molecular dynamics simulation of human prothrombin fragment 1

1995 ◽  
Vol 4 (11) ◽  
pp. 2341-2348 ◽  
Author(s):  
Leping Li ◽  
Tom Darden ◽  
Charles Foley ◽  
Richard Hiskey ◽  
Lee Pedersen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Dynamics Simulation ◽  
Prothrombin Fragment

Molecular Dynamics simulation of organic materials: Structure, potentials and the MiCMoS computer platform

CrystEngComm ◽  
2022 ◽  
Author(s):  
Angelo Gavezzotti ◽  
Leonardo Lo Presti ◽  
Silvia Rizzato
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Determination ◽  
Organic Materials ◽  
Single Point ◽  
Lattice Energy ◽  
Dynamics Simulation ◽  
Organic Crystals ◽  
X Ray ◽  
Point Lattice

The science of organic crystals and materials has seen in a few decades a spectacular improvement from months to minutes for an X-ray structure determination and from single-point lattice energy...

Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

2007 ◽  
Vol 33 (1-2) ◽  
pp. 97-102 ◽  
Author(s):  
Y. Kawashima ◽  
Y. C. Sasaki ◽  
Y. Sugita ◽  
T. Yoda ◽  
Y. Okamoto
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
X Ray
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