PDB_REDO: constructive validation, more than just looking for errors (Q35878830)

10 August 2017

PDB_REDO: constructive validation, more than just looking for errors (English)

1 reference

10 August 2017

4

1 reference

10 August 2017

Robbie P Joosten

1

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author name string

Krista Joosten

series ordinal

2

1 reference

PMCID

3322608

10 August 2017

Garib N Murshudov

series ordinal

3

1 reference

10 August 2017

16 March 2012

1 reference

Acta Crystallographica Section D: Biological Crystallography

10 August 2017

1 reference

10 August 2017

68

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10 August 2017

Pt 4

1 reference

10 August 2017

484-496

1 reference

To B or not to B: a question of resolution?

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Gaia: automated quality assessment of protein structure models

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Characterization of novel StAR (steroidogenic acute regulatory protein) mutations causing non-classic lipoid adrenal hyperplasia

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

REFMAC5 for the refinement of macromolecular crystal structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Overview of the CCP4 suite and current developments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

A series of PDB related databases for everyday needs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Features and development of Coot

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

MolProbity: all-atom structure validation for macromolecular crystallography

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Functional analysis of the Kv1.1 N255D mutation associated with autosomal dominant hypomagnesemia.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Remediation of the protein data bank archive

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Beta-edge interactions in a pentadecameric human antibody V kappa domain

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Artemin crystal structure reveals insights into heparan sulfate binding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

The Uppsala Electron-Density Server

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Coot: model-building tools for molecular graphics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Electron transfer between cytochrome c and cytochome c peroxidase in single crystals

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Refinement of macromolecular structures by the maximum-likelihood method

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Efficient rebuilding of protein structures.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

A self-validation technique for protein structure refinement: the extended Hamilton test.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Announcing the worldwide Protein Data Bank

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Stereochemistry of polypeptide chain configurations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Antibody multispecificity mediated by conformational diversity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Errors in protein structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Improved methods for building protein models in electron density maps and the location of errors in these models

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

Valence screening of water in protein crystals reveals potential Na+ binding sites.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3322608

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

24 September 2018

1 reference

https://api.crossref.org/works/10.1107%2FS0907444911054515

A graphics model building and refinement system for macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS0907444911054515

PDB Improvement Starts with Data Deposition

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS0907444911054515

PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS0907444911054515

Rfreeand theRfreeratio. II. Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS0907444911054515

10.1107/S0907444911054515

21 January 2018

Identifiers

DOI

1 reference

10 August 2017

1 reference

10 August 2017

1 reference

PMCID

3322608