Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. (Q34488156)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180575%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

title

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB (English)

1 reference

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18 February 2020

1 reference

3

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18 February 2020

Pieter M.S. Hendrickx

series ordinal

1

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18 February 2020

Aleksandras Gutmanas

series ordinal

2

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18 February 2020

author name string

Pieter M S Hendrickx

series ordinal

1

1 reference

PubMed publication ID

23180575

2 August 2017

language of work or name

English

0 references

publication date

15 January 2013

1 reference

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18 February 2020

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18 February 2020

volume

81

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18 February 2020

issue

4

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18 February 2020

page(s)

583-591

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CING: an integrated residue-based structure validation program suite

18 February 2020

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6 July 2018

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Reorganizing the protein space at the Universal Protein Resource (UniProt)

6 July 2018

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6 July 2018

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6 July 2018

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The Protein Data Bank in Europe (PDBe): bringing structure to biology

6 July 2018

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SHIFTX2: significantly improved protein chemical shift prediction

6 July 2018

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A novel strategy for NMR resonance assignment and protein structure determination

6 July 2018

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Extending CATH: increasing coverage of the protein structure universe and linking structure with function

6 July 2018

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

6 July 2018

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Validation of archived chemical shifts through atomic coordinates

6 July 2018

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PROSESS: a protein structure evaluation suite and server

6 July 2018

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MolProbity: all-atom structure validation for macromolecular crystallography

6 July 2018

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DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure.

6 July 2018

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The Pfam protein families database

6 July 2018

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

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

6 July 2018

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Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

6 July 2018

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

6 July 2018

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

6 July 2018

1 reference

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Data growth and its impact on the SCOP database: new developments

6 July 2018

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6 July 2018

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

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

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

6 July 2018

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Solution structure of hypothetical protein, HP0495 (Y495_HELPY) from Helicobacter pylori

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

Evaluating protein structures determined by structural genomics consortia

6 July 2018

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The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

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

6 July 2018

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

6 July 2018

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6 July 2018

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Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

6 July 2018

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

6 July 2018

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AstexViewer: a visualisation aid for structure-based drug design

6 July 2018

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

6 July 2018

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BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

6 July 2018

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Dipolar couplings in macromolecular structure determination

6 July 2018

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6 July 2018

The Protein Data Bank

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Order matrix analysis of residual dipolar couplings using singular value decomposition.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

OLDERADO: on-line database of ensemble representatives and domains. On Line Database of Ensemble Representatives And DOmains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

VERIFY3D: assessment of protein models with three-dimensional profiles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

Errors in protein structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

WHAT IF: a molecular modeling and drug design program

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X‐ray structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

The Protein Data Bank: a computer-based archival file for macromolecular structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3618379

The Protein Data Bank: a historical perspective.

6 July 2018

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https://api.crossref.org/works/10.1002%2FPROT.24213

PDBe: Protein Data Bank in Europe

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24213

Quantitative evaluation of experimental NMR restraints.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24213

REDCAT: a residual dipolar coupling analysis tool

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24213

A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24213

Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase

21 January 2018

1 reference

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21 January 2018

Identifiers

DOI

10.1002/PROT.24213

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180575%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

1 reference

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18 February 2020

PubMed publication ID

23180575

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180575%20AND%20SRC:MED&resulttype=core&format=json