CING: an integrated residue-based structure validation program suite (Q41666652)

6 October 2017

CING: an integrated residue-based structure validation program suite (English)

1 reference

6 October 2017

7

1 reference

6 October 2017

Tim J Stevens

6

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Sander B Nabuurs

4

object named as

Sander B Nabuurs

1 reference

6 October 2017

Jurgen F Doreleijers

1

1 reference

6 October 2017

Alan W Sousa da Silva

2

1 reference

6 October 2017

Elmar Krieger

3

1 reference

6 October 2017

Christian A E M Spronk

5

1 reference

6 October 2017

Gert Vriend

8

1 reference

6 October 2017

Geerten W Vuister

9

1 reference

6 October 2017

18 September 2012

1 reference

Journal of Biomolecular NMR

6 October 2017

1 reference

6 October 2017

54

1 reference

6 October 2017

3

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6 October 2017

267-283

1 reference

NMR structure note: solution structure of Ca²⁺ binding domain 2B of the third isoform of the Na⁺/Ca²⁺ exchanger

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Comprehensive automation for NMR structure determination of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Protein structure validation by generalized linear model root-mean-square deviation prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Biomolecules in the computer: Jmol to the rescue

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

A series of PDB related databases for everyday needs

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Validation of archived chemical shifts through atomic coordinates

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Ca2+ regulation in the Na+/Ca2+ exchanger features a dual electrostatic switch mechanism

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Consistent blind protein structure generation from NMR chemical shift data

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Remediation of the protein data bank archive

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Benchmarking consensus model quality assessment for protein fold recognition.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Evaluating protein structures determined by structural genomics consortia

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

The Amber biomolecular simulation programs

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Weak alignment NMR: a hawk-eyed view of biomolecular structure

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

NMR data collection and analysis protocol for high-throughput protein structure determination

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Automated NMR structure calculation with CYANA

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Announcing the worldwide Protein Data Bank

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

RefDB: a database of uniformly referenced protein chemical shifts

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Structural quality assurance

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Close-range electrostatic interactions in proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Disulfide recognition in an optimized threading potential.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Objectively judging the quality of a protein structure from a Ramachandran plot

6 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

6 June 2018

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

MOLMOL: a program for display and analysis of macromolecular structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Errors in protein structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Conformation of amino acid side-chains in proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

In defence of our science - validation now!

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Multi-template approach to modeling engineered disulfide bonds.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

DRESS: a database of REfined solution NMR structures.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Quantitative evaluation of experimental NMR restraints.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Quality assessment of NMR structures: a statistical survey

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3483101

Cython: The Best of Both Worlds

30 September 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

Application of the random coil index to studying protein flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

Python for Scientists and Engineers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

Who checks the checkers? four validation tools applied to eight atomic resolution structures 1 1Edited by I. A. Wilson

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10858-012-9669-7

Improving the quality of protein structures derived by NMR spectroscopy

21 January 2018

1 reference

12 December 2020

Automated structure determination from NMR spectra

1 reference

12 December 2020

NOE assignment with ARIA 2.0: the nuts and bolts

1 reference

12 December 2020

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

1 reference

12 December 2020

Assessing precision and accuracy of protein structures derived from NMR data

1 reference

12 December 2020

Ca2+ regulation in the Na+/Ca2+ exchanger involves two markedly different Ca2+ sensors

1 reference

12 December 2020

10.1007/S10858-012-9669-7

Identifiers

DOI

1 reference

Dimensions Publication ID

6 October 2017

0 references

1 reference

6 October 2017

PubMed publication ID

22986687

1 reference