Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining (Q30411764)

17 October 2017

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining (English)

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17 October 2017

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3

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Alexander Wlodawer

2

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Bernhard Rupp

object named as

Bernhard Rupp

5

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Mariusz Jaskólski

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Mariusz Jaskolski

4

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Zbigniew Dauter

1

object named as

Zbigniew Dauter

1 reference

17 October 2017

14 April 2014

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17 October 2017

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17 October 2017

1

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17 October 2017

Pt 3

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17 October 2017

179-193

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Weak data do not make a free lunch, only a cheap meal

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

A challenging interpretation of a hexagonally layered protein structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

The future of crystallography in drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

The quality and validation of structures from structural genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Peptide-based inhibitors of Plk1 polo-box domain containing mono-anionic phosphothreonine esters and their pivaloyloxymethyl prodrugs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Recommendations of the wwPDB NMR Validation Task Force

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Better models by discarding data?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

How good are my data and what is the resolution?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

On optimal placement of molecules in the unit cell

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Structural and thermodynamic characterization of Nore1-SARAH: a small, helical module important in signal transduction networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Out-of-register -sheets suggest a pathway to toxic amyloid aggregates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Linking Crystallographic Model and Data Quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

PDB_REDO: constructive validation, more than just looking for errors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Outcome of the first electron microscopy validation task force meeting

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Diverse peptide presentation of rhesus macaque major histocompatibility complex class I Mamu-A 02 revealed by two peptide complex structures and insights into immune escape of simian immunodeficiency virus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Crystal structure of small protein crambin at 0.48 Å resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

An introduction to data reduction: space-group determination, scaling and intensity statistics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Structural and Functional Characterization of a Highly Specific Serpin in the Insect Innate Immunity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Unmet challenges of structural genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Radiation stability of proteinase K crystals grown by LB nanotemplate method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Data deposition and annotation at the worldwide protein data bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Draft Crystal Structure of the Vault Shell at 9-Å Resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Inference of macromolecular assemblies from crystalline state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Five retracted structure reports: inverted or incorrect?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Structure of a bacterial multidrug ABC transporter

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Scaling and assessment of data quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

The Uppsala Electron-Density Server

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Structural basis for transcription regulation by alarmone ppGpp.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Announcing the worldwide Protein Data Bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Crystal structure of Klebsiella aerogenes UreE, a nickel-binding metallochaperone for urease activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Why protein crystals favour some space-groups over others

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Studies on the inhibitory action of mercury upon proteinase K

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Solvent content of protein crystals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4086436

Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins

20 June 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

Studies of NaCl-KCl Solid Solutions. I. Heats of Formation, Lattice Spacings, Densities, Schottky Defects and Mutual Solubilities1,2

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

An Essay towards Solving a Problem in the Doctrine of Chances. By the Late Rev. Mr. Bayes, F. R. S. Communicated by Mr. Price, in a Letter to John Canton, A. M. F. R. S

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

On the propagation of errors

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

The Influence of Prior Beliefs on Scientific Judgments of Evidence Quality

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

Statistical quality indicators for electron-density maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

Between objectivity and subjectivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514005442

Real-space solution to the problem of full disclosure

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25075337

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Polyamines stabilize left-handed Z-DNA: using X-ray crystallographic analysis, we have found a new type of polyamine (PA) that stabilizes left-handed Z-DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25075337

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S2052252514005442

1 reference

17 October 2017

1 reference

17 October 2017

1 reference

PMCID

4086436