scholarly journals Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

2017 ◽  
Vol 9 (6) ◽  
pp. 877-893 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
Keyword(s):  
Protein Dynamics ◽  
Protein Data Bank ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Data Bank ◽  
Mode Analysis

scholarly journals An Algorithm to Predict the Possible SARS-CoV-2 Mutations

2021 ◽  
Vol 3 (1) ◽  
pp. 1-7
Author(s):  
Raúl Isea
Keyword(s):  
Free Energy ◽  
Protein Data Bank ◽  
Gibbs Free Energy ◽  
Human Population ◽  
Normal Mode Analysis ◽  
Network Models ◽  
Data Bank ◽  
Mode Analysis ◽  
Vibration Modes ◽  
Anisotropic Network

An algorithm to determine the possible mutations that can occur in the S protein responsible of the Covid-19 in humans is designed. To do that, nine tridimensional sequences available in the Protein Data Bank similar to the initial strain sequenced in Wuhan (December 2019) are identified. The conditions driving this potential mutation are: (1) an accumulated number of mutations greater than (or equal to) 5 in each position; (2), a cumulative value of the different variations of Gibbs free energy less than -2.0 Kcal/mol; and (3), a squared fluctuation greater than 1.6 Å obtained according to calculations for normal mode analysis based on anisotropic network models (ANM) after averaging the first 20 vibration modes. The result is that 491 positions can mutate, while 424 positions did not provide any mutation. Finally, the results reveal that there are mutations that cannot be predicted, so more studies are needed to determine why they are present in the human population.

Normal mode analysis of protein dynamics in a non-Eckart frame

2010 ◽  
Vol 132 (10) ◽  
pp. 104109 ◽  
Author(s):  
Sotaro Fuchigami ◽  
Satoshi Omori ◽  
Mitsunori Ikeguchi ◽  
Akinori Kidera
Keyword(s):  
Protein Dynamics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis
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