[NMR paper] Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1
Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1
Protein structures calculated using NMR data are less accurate and less well-defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way and show that the structures generated are more accurate and better...
nmrlearner
Journal club
0
06-14-2023 10:14 PM
Improved validation of IDP ensembles by one-bond Cαâ??Hα scalar couplings
Improved validation of IDP ensembles by one-bond Cαâ??Hα scalar couplings
Abstract
Intrinsically disordered proteins (IDPs) are best described by ensembles of conformations and a variety of approaches have been developed to determine IDP ensembles. Because of the large number of conformations, however, cross-validation of the determined ensembles by independent experimental data is crucial. The 1JCαHα coupling constant is particularly suited for cross-validation, because it has a large magnitude and mostly depends on the often less accessible...
nmrlearner
Journal club
0
10-04-2015 02:58 PM
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
Abstract
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to...
nmrlearner
Journal club
0
04-11-2015 12:04 AM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
J Am Chem Soc. 2011 Apr 4;
Authors: Ryabov Y, Schwieters CD, Clore GM
(15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...
nmrlearner
Journal club
0
04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201020c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ
nmrlearner
Journal club
0
04-05-2011 10:37 AM
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
J Am Chem Soc. 2011 Mar 24;
Authors: Linser R, Bardiaux B, Higman V, Fink U, Reif B
Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane...
nmrlearner
Journal club
0
03-26-2011 07:00 PM
Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy
Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy
Rasmus Linser, Benjamin Bardiaux, Victoria Higman, Uwe Fink and Bernd Reif
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja110222h/aop/images/medium/ja-2010-10222h_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja110222h
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/Dh0EBf8PwcY
nmrlearner
Journal club
0
03-24-2011 08:02 PM
Protein structure calculation with data imputation: the use of substitute restraints
Protein structure calculation with data imputation: the use of substitute restraints
Abstract The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It...
Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation ... - ScienceDirect.com
Linear Mode
