Path Energy Minimization: A New Method for the Simulation of Conformational Transitions of Large Molecules

2007 ◽  
pp. 215-240
Author(s):  
Oliver S. Smart
Keyword(s):  
Energy Minimization ◽  
Conformational Transitions ◽  
New Method ◽  
Large Molecules

The effective group potential, a new method for the study of spectrum in large molecules: Tests and perspectives

2002 ◽  
Vol 116 (12) ◽  
pp. 4829 ◽  
Author(s):  
Jean-Louis Heully ◽  
Romuald Poteau ◽  
Sandra Berasaluce ◽  
Fabienne Alary
Keyword(s):  
New Method ◽  
Large Molecules ◽  
Effective Group

Testing the method of crystallographic refinement using molecular dynamics

1989 ◽  
Vol 22 (1) ◽  
pp. 1-8 ◽  
Author(s):  
M. Fujinaga ◽  
P. Gros ◽  
W. F. van Gunsteren
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Phospholipase A2 ◽  
Conformational Transitions ◽  
New Method ◽  
High Resolution Data ◽  
Manual Intervention ◽  
Isomorphous Replacement ◽  
Simulation Package ◽  
Resolution Data

The method of crystallographic refinement using molecular dynamics [Brünger, Kuriyan & Karplus (1987). Science, 235, 458–460] has been implemented to work with the GROMOS simulation package. It has been tested by applying it to the structure of phospholipase A2. The structure of this molecule had previously been refined at high resolution with conventional methods. The new method successfully refined the initial multi-isomorphous replacement structure, removing most of the errors, without any manual intervention. All the refinement was performed at 300 K. The use of lower-resolution data allows greater conformational transitions to occur whereas the inclusion of high-resolution data results in a more accurate structure.

scholarly journals The effect of ultrasound as a new method of studying conformational transitions in enzyme active sites

FEBS Letters ◽  
1975 ◽  
Vol 49 (3) ◽  
pp. 325-328 ◽  
Author(s):  
I.V. Berezin ◽  
A.M. Klibanov ◽  
A.A. Klyosov ◽  
Karel Martinek ◽  
V.K. Švedas
Keyword(s):  
Active Sites ◽  
Conformational Transitions ◽  
New Method ◽  
Enzyme Active Sites

ViBe with Adaptive Threshold Based on Energy Minimization

2015 ◽  
Vol 782 ◽  
pp. 326-334
Author(s):  
Liang Xie ◽  
Xiao Hu Zhang ◽  
Peng Yu Guo ◽  
Gu Can Long
Keyword(s):  
Real World ◽  
Background Subtraction ◽  
Energy Minimization ◽  
Spatial Information ◽  
Adaptive Threshold ◽  
New Method ◽  
Kernel Estimates ◽  
Visual Background ◽  
Synthetic Test ◽  
Better Than

VIsual Background Extractor (VIBe) is a simple and effective background subtraction model, it is important to choose the threshold according to different environments. A new method based on the VIBe is presented which uses the adaptive threshold. We give a new description of the similarity degree without threshold, and then use the energy minimization model to combine the spatial information and show that dynamically choosing threshold in our kernel estimates at each individual pixel can significantly improve results. To compare with the traditional VIBe algorithms, a synthetic test SABS and a real world test I2R are used. Experiment shows that the presented method is on average 10% better than the traditional VIBe in accuracy.

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