scholarly journals Quantitative Residue-Specific Protein Backbone Torsion Angle Dynamics from Concerted Measurement of 3J Couplings

2015 ◽  
Vol 137 (4) ◽  
pp. 1432-1435 ◽  
Author(s):  
Jung Ho Lee ◽  
Fang Li ◽  
Alexander Grishaev ◽  
Ad Bax
Keyword(s):  
Torsion Angle ◽  
Specific Protein ◽  
Protein Backbone ◽  
Backbone Torsion Angle

scholarly journals TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e30361 ◽  
Author(s):  
Jiangning Song ◽  
Hao Tan ◽  
Mingjun Wang ◽  
Geoffrey I. Webb ◽  
Tatsuya Akutsu
Keyword(s):  
Support Vector Regression ◽  
Torsion Angle ◽  
Support Vector ◽  
Protein Backbone ◽  
Regression Approach ◽  
Backbone Torsion Angle

scholarly journals The Fastest Simulation of Protein Folding Based on Torsion Angles

2020 ◽  
Author(s):  
Seonghoon Jeong
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Potential Energy ◽  
Torsion Angle ◽  
Stable State ◽  
Protein Backbone ◽  
Torsion Angles ◽  
Backbone Torsion Angle ◽  
Torsional Inertia ◽  
And Function

Abstract Backgrounds: Enormous number of possible conformations in the protein structure simulation have led molecular dynamics researchers to be frustrated until now. Some methods with defects ended their experiments into failure. This made them fail to determine the structure and function of folded protein in stable state with the lowest potential energy. This apparently exist in nature. The purpose of resolving a protein folding pathway that follows protein backbone residues torsional inertia was accomplished. Results A new method, torsion angle modeling, was adopted focused on the rotation of dihedral angles. The potential energy was calculated by rotating torsion angles of the peptide with 8 residues. It was found that when moving in the order of torsional inertia, 8 residues swivel in sequence. Six passes were repeated to find the lowest value. Conclusion The protein backbone torsion angle plays very important role in predicting protein structure. Actually it was thousand times faster or more than others to get the obvious pathway.

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

scholarly journals Change in backbone torsion angle distribution on protein folding

2000 ◽  
Vol 9 (6) ◽  
pp. 1129-1136 ◽  
Author(s):  
Andrei-José Petrescu ◽  
Patrick Calmettes ◽  
Dominique Durand ◽  
Veronique Receveur ◽  
Jeremy C. Smith
Keyword(s):  
Protein Folding ◽  
Torsion Angle ◽  
Angle Distribution ◽  
Backbone Torsion Angle

Relationships between amino acid sequence and backbone torsion angle preferences

2004 ◽  
Vol 55 (4) ◽  
pp. 992-998 ◽  
Author(s):  
O. Keskin ◽  
D. Yuret ◽  
A. Gursoy ◽  
M. Turkay ◽  
B. Erman
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Torsion Angle ◽  
Backbone Torsion Angle

scholarly journals ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

2019 ◽  
Vol 16 (1) ◽  
pp. 528-552 ◽  
Author(s):  
Chuan Tian ◽  
Koushik Kasavajhala ◽  
Kellon A. A. Belfon ◽  
Lauren Raguette ◽  
He Huang ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Amino Acid ◽  
Specific Protein ◽  
Protein Backbone ◽  
Energy Surfaces

Determination of the backbone torsion angle ? in nucleic acids

1994 ◽  
Vol 4 (5) ◽  
pp. 595-601 ◽  
Author(s):  
M. J. J. Blommers ◽  
D. Nanz ◽  
O. Zerbe
Keyword(s):  
Nucleic Acids ◽  
Torsion Angle ◽  
Backbone Torsion Angle
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