(Q38123436)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

title

An overview of tools for the validation of protein NMR structures (English)

1 reference

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5 March 2020

1

1 reference

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5 March 2020

Pieter M.S. Hendrickx

3

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5 March 2020

Aleksandras Gutmanas

5

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5 March 2020

author name string

Rasmus H Fogh

2

1 reference

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5 March 2020

Jurgen F Doreleijers

4

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5 March 2020

publication date

23 July 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

Journal of Biomolecular NMR

5 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

volume

58

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

issue

4

1 reference

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5 March 2020

page(s)

259-285

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1007/s10858-013-9750-x

5 March 2020

exact match

0 references

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Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability

21 January 2018

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KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program

21 January 2018

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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

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21 January 2018

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The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

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CING: an integrated residue-based structure validation program suite

21 January 2018

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NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.

21 January 2018

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VERIFY3D: assessment of protein models with three-dimensional profiles

21 January 2018

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Accurate bond and angle parameters for X-ray protein structure refinement

21 January 2018

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A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints

21 January 2018

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CheckShift: automatic correction of inconsistent chemical shift referencing

21 January 2018

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CheckShift improved: fast chemical shift reference correction with high accuracy

21 January 2018

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Implementing an X-ray validation pipeline for the Protein Data Bank

21 January 2018

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Structure calculation of biological macromolecules from NMR data.

21 January 2018

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Torsion angle dynamics for NMR structure calculation with the new program DYANA

21 January 2018

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SHIFTX2: significantly improved protein chemical shift prediction

21 January 2018

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NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.

21 January 2018

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Outcome of the first electron microscopy validation task force meeting

21 January 2018

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Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

21 January 2018

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Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA

21 January 2018

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Errors in protein structures

21 January 2018

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Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics

21 January 2018

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Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

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AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR

21 January 2018

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A novel strategy for NMR resonance assignment and protein structure determination

21 January 2018

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21 January 2018

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Simultaneous determination of protein structure and dynamics.

21 January 2018

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Refinement of protein structures in explicit solvent

21 January 2018

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Automated protein structure determination from NMR spectra.

21 January 2018

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Structure validation by Calpha geometry: phi,psi and Cbeta deviation

21 January 2018

1 reference

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Antiparallel coiled-coil-mediated dimerization of myosin X

21 January 2018

1 reference

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Improved technologies now routinely provide protein NMR structures useful for molecular replacement

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

The PSIPRED protein structure prediction server

21 January 2018

1 reference

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PROSHIFT: Protein chemical shift prediction using artificial neural networks

21 January 2018

1 reference

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Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

21 January 2018

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A new model for chemical shifts of amide hydrogens in proteins

21 January 2018

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Assignment validation software suite for the evaluation and presentation of protein resonance assignment data

21 January 2018

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A large-scale experiment to assess protein structure prediction methods.

21 January 2018

1 reference

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Critical assessment of methods of protein structure prediction (CASP)--round IX

21 January 2018

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Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts.

21 January 2018

1 reference

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Quantitative evaluation of experimental NMR restraints.

21 January 2018

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DRESS: a database of REfined solution NMR structures.

21 January 2018

1 reference

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Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

21 January 2018

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Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

21 January 2018

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New parameters for the refinement of nucleic acid-containing structures

21 January 2018

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HARMONY: a server for the assessment of protein structures.

21 January 2018

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A new generation of crystallographic validation tools for the protein data bank

21 January 2018

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RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

21 January 2018

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Inferential structure determination.

21 January 2018

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ARIA2: automated NOE assignment and data integration in NMR structure calculation

21 January 2018

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CASD-NMR: critical assessment of automated structure determination by NMR

21 January 2018

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Blind testing of routine, fully automated determination of protein structures from NMR data

21 January 2018

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Structure-based prediction of methyl chemical shifts in proteins

21 January 2018

1 reference

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Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.

21 January 2018

1 reference

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A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics

21 January 2018

1 reference

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A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data.

21 January 2018

1 reference

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RosettaHoles2: a volumetric packing measure for protein structure refinement and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Consistent blind protein structure generation from NMR chemical shift data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

De novo protein structure generation from incomplete chemical shift assignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Structure and functional analysis of the MYND domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.

21 January 2018

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https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy

21 January 2018

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Refinement of protein structure against non-redundant carbonyl 13C NMR relaxation.

21 January 2018

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Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

21 January 2018

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21 January 2018

1 reference

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PDBe: Protein Data Bank in Europe

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

The CCPN data model for NMR spectroscopy: development of a software pipeline

21 January 2018

1 reference

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WHAT IF: a molecular modeling and drug design program

21 January 2018

1 reference

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Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications

21 January 2018

1 reference

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A probabilistic approach for validating protein NMR chemical shift assignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Importance of the C-terminal loop L137-S141 for the folding and folding stability of staphylococcal nuclease

21 January 2018

1 reference

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ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

21 January 2018

1 reference

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VADAR: a web server for quantitative evaluation of protein structure quality

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data

21 January 2018

1 reference

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Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

21 January 2018

1 reference

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Automated prediction of 15N, 13Calpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

RefDB: a database of uniformly referenced protein chemical shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Measurement of Structural Restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Interhelical angles in the solution structure of the oligomerization domain of p53: correction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Flipping a genetic switch by subunit exchange

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-013-9750-X

Flipping a genetic switch by subunit exchange

21 January 2018

1 reference

12 December 2020

Recommendations of the wwPDB NMR Validation Task Force

1 reference

12 December 2020

4D prediction of protein (1)H chemical shifts

1 reference

12 December 2020

Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins

1 reference

12 December 2020

Validation of archived chemical shifts through atomic coordinates

1 reference

12 December 2020

Influence of the distance of the proline carbonyl from the beta and gamma carbon on the 13C chemical shifts

1 reference

12 December 2020

Retraction notice to "Structure and functional analysis of the MYND domain" [J. Mol. Biol. (2006) 358, 498-508]

1 reference

12 December 2020

Improving the quality of protein structures derived by NMR spectroscopy

1 reference

12 December 2020

An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies

1 reference

12 December 2020

Definition of a new information-based per-residue quality parameter

1 reference

12 December 2020

10.1007/S10858-013-9750-X

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23877928%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1 reference