Conformational analysis of protein structures derived from NMR data

1993 ◽  
Vol 17 (3) ◽  
pp. 232-251 ◽  
Author(s):  
Malcolm W. MacArthur ◽  
Janet M. Thornton
Keyword(s):  
Conformational Analysis ◽  
Protein Structures ◽  
Nmr Data

scholarly journals NMR Protein Structure Calculation and Sphere Intersections

2020 ◽  
Vol 8 (1) ◽  
pp. 89-101
Author(s):  
Carlile Lavor ◽  
Rafael Alves ◽  
Michael Souza ◽  
Luis Aragón José
Keyword(s):  
Protein Structures ◽  
Structure Calculation ◽  
Bp Algorithm ◽  
Main Step ◽  
Combinatorial Method ◽  
Nmr Data ◽  
Sampling Process ◽  
Protein Molecules ◽  
Protein Structure Calculation ◽  
Branch And Prune

AbstractNuclear Magnetic Resonance (NMR) experiments can be used to calculate 3D protein structures and geometric properties of protein molecules allow us to solve the problem iteratively using a combinatorial method, called Branch-and-Prune (BP). The main step of BP algorithm is to intersect three spheres centered at the positions for atoms i − 3, i − 2, i − 1, with radii given by the atomic distances di−3,i, di−2,i, di−1,i, respectively, to obtain the position for atom i. Because of uncertainty in NMR data, some of the distances di−3,i should be represented as interval distances [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}], where {\underline{d}_{i - 3,i}} \le {d_{i - 3,i}} \le {\bar d_{i - 3,i}}. In the literature, an extension of the BP algorithm was proposed to deal with interval distances, where the idea is to sample values from [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}]. We present a new method, based on conformal geometric algebra, to reduce the size of [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}], before the sampling process. We also compare it with another approach proposed in the literature.

Calculating Protein Structures from NMR Data

2003 ◽  
pp. 157-194 ◽  
Author(s):  
Peter Güntert
Keyword(s):  
Protein Structures ◽  
Nmr Data

The precision of protein structures determined from NMR data: Reality or illusion?

Proteins ◽  
1991 ◽  
pp. 110-115 ◽  
Author(s):  
Timothy F. Havel
Keyword(s):  
Protein Structures ◽  
Nmr Data

Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data

2005 ◽  
Vol 127 (47) ◽  
pp. 16621-16628 ◽  
Author(s):  
Alexander Grishaev ◽  
Justin Wu ◽  
Jill Trewhella ◽  
Ad Bax
Keyword(s):  
Small Angle ◽  
Protein Structures ◽  
Multidomain Protein ◽  
X Ray ◽  
X Ray Scattering ◽  
Nmr Data ◽  
Ray Scattering

Conformational Analysis of Open-Chain 1,2:3,4-Diepoxides: Comparison of crystal structures, NMR data, and molecular-orbital calculations

1993 ◽  
Vol 76 (5) ◽  
pp. 1863-1875 ◽  
Author(s):  
Daniel Bur ◽  
Martin Nikles ◽  
Urs Séquin ◽  
Markus Neuburger ◽  
Margareta Zehnder
Keyword(s):  
Conformational Analysis ◽  
Crystal Structures ◽  
Molecular Orbital ◽  
Molecular Orbital Calculations ◽  
Open Chain ◽  
Nmr Data

SESAME: A least-squares approach to the evaluation of protein structures computed from NMR data

1993 ◽  
Vol 3 (3) ◽  
pp. 355-360 ◽  
Author(s):  
Ju-xing Yang ◽  
T.F. Havel
Keyword(s):  
Least Squares ◽  
Protein Structures ◽  
Nmr Data ◽  
Least Squares Approach

Comparison of Protein Structures in Solution Using Local Conformations Derived from NMR Data: Application to Cytochromec

1994 ◽  
Vol 12 (3) ◽  
pp. 527-558 ◽  
Author(s):  
Leela Kar ◽  
Simon A. Sherman ◽  
Michael E. Johnson
Keyword(s):  
Protein Structures ◽  
Nmr Data ◽  
Data Application ◽  
Local Conformations

scholarly journals Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Structure ◽  
2012 ◽  
Vol 20 (2) ◽  
pp. 227-236 ◽  
Author(s):  
Antonio Rosato ◽  
James M. Aramini ◽  
Cheryl Arrowsmith ◽  
Anurag Bagaria ◽  
David Baker ◽  
...  
Keyword(s):  
Protein Structures ◽  
Nmr Data ◽  
Automated Determination

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

2005 ◽  
Vol 31 (1) ◽  
pp. 59-64 ◽  
Author(s):  
Jianhan Chen ◽  
Hyung-Sik Won ◽  
Wonpil Im ◽  
H. Jane Dyson ◽  
Charles L. Brooks
Keyword(s):  
Force Fields ◽  
Protein Structures ◽  
Conformational Sampling ◽  
Nmr Data
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