Prediction of protein flexibility using a conformationally restrained contact map

2018 ◽  
Vol 86 (10) ◽  
pp. 1111-1116
Author(s):  
Rebecca Vera ◽  
Melissa Synsmir-Zizzamia ◽  
Sarah Ojinnaka ◽  
David A. Snyder
Keyword(s):  
Protein Flexibility ◽  
Contact Map ◽  
Conformationally Restrained

A Divide-and-Conquer Strategy for the Prediction of Protein Contact Map

2014 ◽  
Vol 12 (2) ◽  
pp. 124-130 ◽  
Author(s):  
Cosme Santiesteban-Toca ◽  
Gerardo Casanola-Martin ◽  
Jesus Aguilar-Ruiz
Keyword(s):  
Divide And Conquer ◽  
Contact Map

scholarly journals Contact map based crystal structure prediction using global optimization

CrystEngComm ◽  
2021 ◽  
Author(s):  
Jianjun Hu ◽  
Wenhui Yang ◽  
Rongzhi Dong ◽  
Yuxin Li ◽  
Xiang Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Global Optimization ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
New Materials ◽  
Contact Map

Crystal structure prediction is now playing an increasingly important role in the discovery of new materials or crystal engineering.

ChemInform Abstract: Reversible Inhibitors of the Gastric (H+/K+)-ATPase. Part 1. 1-Aryl-4-methylpyrrolo(3,2-c)quinolines as Conformationally Restrained Analogues of 4-(Arylamino)quinolines.

ChemInform ◽  
1990 ◽  
Vol 21 (24) ◽  
Author(s):  
T. H. BROWN ◽  
R. J. IFE ◽  
D. J. KEELING ◽  
S. M. LAING ◽  
C. A. LEACH ◽  
...  
Keyword(s):  
Reversible Inhibitors ◽  
Conformationally Restrained

scholarly journals Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1484
Author(s):  
Christopher Reinknecht ◽  
Anthony Riga ◽  
Jasmin Rivera ◽  
David A. Snyder
Keyword(s):  
Protein Flexibility ◽  
Molecular Machines ◽  
Md Simulations ◽  
Peptide Bond ◽  
Structure Calculation ◽  
Atomic Scale ◽  
Heavy Atoms ◽  
Structural Ensembles ◽  
Atomic Coordinates ◽  
Motional Behavior

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.

Site-Specific Coupling of Hydration Water and Protein Flexibility Studied in Solution with Ultrafast 2D-IR Spectroscopy

2012 ◽  
Vol 134 (45) ◽  
pp. 18705-18712 ◽  
Author(s):  
John T. King ◽  
Kevin J. Kubarych
Keyword(s):  
Ir Spectroscopy ◽  
Protein Flexibility ◽  
Hydration Water ◽  
Site Specific ◽  
2D Ir

Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy

2021 ◽  
pp. 113302
Author(s):  
Milind Jagota ◽  
Raphael J.L. Townshend ◽  
Lin-Woo Kang ◽  
David A. Bushnell ◽  
Ron O. Dror ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Gold Nanoparticles ◽  
Protein Flexibility ◽  
Cryo Electron Microscopy

Protein Flexibility and Adaptability Seen in 25 Crystal Forms of T4 Lysozyme

1995 ◽  
Vol 250 (4) ◽  
pp. 527-552 ◽  
Author(s):  
Xue-jun Zhang ◽  
Joan A. Wozniak ◽  
Brian W. Matthews
Keyword(s):  
Protein Flexibility ◽  
T4 Lysozyme ◽  
Crystal Forms

Roles of Fe-His Bonds in stability of Hemoglobin: Recognition of Protein Flexibility by Q Sepharose

2021 ◽  
Author(s):  
S. Nagatomo ◽  
T. Kitagawa ◽  
M. Nagai
Keyword(s):  
Protein Flexibility
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