PDB_REDO: automated re-refinement of X-ray structure models in the PDB. (Q40010362)

16 September 2017

PDB_REDO: automated re-refinement of X-ray structure models in the PDB. (English)

1 reference

16 September 2017

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7

Erik Bongcam-Rudloff

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Robbie P. Joosten

Robbie P Joosten

1

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Andreas Gisel

Andreas Gisel

15

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Ian J Tickle

Ian J Tickle

23

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Heinz Stockinger

Heinz Stockinger

4

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Marco Pagni

Marco Pagni

20

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Gilbert Deleage

Gilbert Deleage

10

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author name string

Jean Salzemann

2

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16 September 2017

Vincent Bloch

3

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16 September 2017

Ann-Charlott Berglund

5

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16 September 2017

Christophe Blanchet

6

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16 September 2017

Christophe Combet

8

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16 September 2017

Ana L Da Costa

9

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16 September 2017

Matteo Diarena

11

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16 September 2017

Roberto Fabbretti

12

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16 September 2017

Géraldine Fettahi

13

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16 September 2017

Volker Flegel

14

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16 September 2017

Vinod Kasam

16

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16 September 2017

Timo Kervinen

17

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16 September 2017

Eija Korpelainen

18

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16 September 2017

Kimmo Mattila

19

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16 September 2017

Matthieu Reichstadt

21

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16 September 2017

Vincent Breton

22

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16 September 2017

Gert Vriend

24

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16 September 2017

3 April 2009

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Journal of Applied Crystallography

16 September 2017

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16 September 2017

42

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16 September 2017

Pt 3

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16 September 2017

376-384

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

16 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

SHELXL: high-resolution refinement

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Remediation of the protein data bank archive

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

A flexible approach to induced fit docking

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Grid-enabled high-throughput in silico screening against influenza A neuraminidase.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

The Uppsala Electron-Density Server

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Making optimal use of empirical energy functions: force-field parameterization in crystal space

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

The CCP4 suite: programs for protein crystallography

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Announcing the worldwide Protein Data Bank

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Homo crystallographicus--quo vadis?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Experimentally observed conformation-dependent geometry and hidden strain in proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Errors in protein structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Where freedom is given, liberties are taken

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

DRESS: a database of REfined solution NMR structures.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246819

Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22477769

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

[23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22477769

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S0021889809008784

1 reference

16 September 2017

1 reference

16 September 2017

PubMed publication ID

22477769

1 reference