The Protein Data Bank in Europe (PDBe): bringing structure to biology (Q33453545)

26 July 2017

title

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

1 reference

26 July 2017

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2

1 reference

26 July 2017

Sameer Velankar

1

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publication date

18 March 2011

1 reference

Acta Crystallographica Section D: Biological Crystallography

26 July 2017

published in

1 reference

26 July 2017

volume

67

1 reference

26 July 2017

issue

Pt 4

1 reference

26 July 2017

page(s)

324-330

1 reference

EMDataBank.org: unified data resource for CryoEM

26 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Straightforward and complete deposition of NMR data to the PDBe

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Validation of archived chemical shifts through atomic coordinates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The European Bioinformatics Institute's data resources

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The Pfam protein families database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Chemical Entities of Biological Interest: an update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The IntAct molecular interaction database in 2010

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Relationship between chemical shift value and accessible surface area for all amino acid atoms.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

On vital aid: the why, what and how of validation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Reactome knowledgebase of human biological pathways and processes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The GOA database in 2009--an integrated Gene Ontology Annotation resource

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

InterPro: the integrative protein signature database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The Universal Protein Resource (UniProt) 2009

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

MSDmotif: exploring protein sites and motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Protein structure databases with new web services for structural biology and biomedical research

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

A global analysis of NMR distance constraints from the PDB.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Inference of macromolecular assemblies from crystalline state

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Crystallographic refinement of ligand complexes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

A nomenclature and data model to describe NMR experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The RCSB PDB information portal for structural genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

E-MSD: improving data deposition and structure quality

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

E-MSD: an integrated data resource for bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The Uppsala Electron-Density Server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Retrieval of crystallographically-derived molecular geometry information.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

IntEnz, the integrated relational enzyme database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

New electron microscopy database and deposition system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The distributed annotation system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

Rapid and sensitive protein similarity searches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069747

The Protein Data Bank: a historical perspective

21 June 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

Safeguarding the integrity of protein archive

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

Chemical substructure search in SQL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

PQS: a protein quaternary structure file server

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

DRESS: a database of REfined solution NMR structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

PDBe: Protein Data Bank in Europe

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

PDBe: Protein Data Bank in Europe

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions in Native States of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS090744491004117X

Bioinformatics: biology by other means

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21460450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21460450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genome analysis at your fingertips

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21460450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S090744491004117X

1 reference

26 July 2017

1 reference

26 July 2017

1 reference