A new generation of crystallographic validation tools for the protein data bank (Q24634970)

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Language	Label	Description	Also known as
English	A new generation of crystallographic validation tools for the protein data bank	scientific article

Statements

scholarly article

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

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structural biology

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Protein Data Bank

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5

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Zbyszek Otwinowski

10

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Anastassis Perrakis

11

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Jane Shelby Richardson

12

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16

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Robbie P. Joosten

object named as

Robbie P Joosten

6

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Thomas Lütteke

object named as

Thomas Lütteke

9

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Gerard Kleywegt

object named as

Gerard J Kleywegt

7

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object named as

Paul D Adams

2

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object named as

Randy J Read

1

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Axel T. Brunger

object named as

Axel T Brunger

4

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object named as

Ian J Tickle

15

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W Bryan Arendall

3

object named as

W Bryan Arendall

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17

object named as

Peter H Zwart

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14

object named as

Janet L Smith

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author name string

Eugene B Krissinel

8

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William H Sheffler

13

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language of work or name

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publication date

12 October 2011

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19

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10

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1395-412

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RosettaHoles2: a volumetric packing measure for protein structure refinement and validation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

PHENIX: a comprehensive Python-based system for macromolecular structure solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

MolProbity: all-atom structure validation for macromolecular crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Remediation of the protein data bank archive

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

SHELXL: high-resolution refinement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Scaling and assessment of data quality

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

The CCP4 suite: programs for protein crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Errors in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Stereochemical quality of protein structure coordinates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Announcing the worldwide Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Stereochemistry of polypeptide chain configurations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Phi/psi-chology: Ramachandran revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Public access to X-ray diffraction data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Small revisions to predicted distances around metal sites in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

The penultimate rotamer library

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

Detecting and overcoming crystal twinning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Detection and correction of underassigned rotational symmetry prior to structure deposition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Conformation dependence of backbone geometry in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Autoindexing the diffraction patterns from crystals with a pseudotranslation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Analysis and validation of carbohydrate three-dimensional structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Limitations and lessons in the use of X-ray structural information in drug design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Data mining of metal ion environments present in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

ValLigURL: a server for ligand-structure comparison and validation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Crystallographic refinement of ligand complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

A test of enhancing model accuracy in high-throughput crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

The Uppsala Electron-Density Server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Retrieval of crystallographically-derived molecular geometry information.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Choice of data-collection parameters based on statistic modelling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Application and limitations of X-ray crystallographic data in structure-based ligand and drug design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Validation of protein crystal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Detecting outliers in non-redundant diffraction data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Not your average density.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Bayesian statistical analysis of protein side‐chain rotamer preferences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

27 September 2017

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

30 May 2018

Crystallography: crystallographic evidence for deviating C3b structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

30 May 2018

Intensity statistics in twinned crystals with examples from the PDB.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

30 May 2018

Sorting the chaff from the wheat at the PDB.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

PDB Improvement Starts with Data Deposition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

Building meaningful models of glycoproteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

New parameters for the refinement of nucleic acid-containing structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

A re-evaluation of the crystal structure of chloromuconate cycloisomerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

Introduction to twinning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

Validation of protein models from Cα coordinates alone

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195755

28 November 2018

Retraction: Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 A resolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/22000512

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting local structural changes that result from point mutations

1 reference

https://pubmed.ncbi.nlm.nih.gov/22000512

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The penultimate rotamer library

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

[22] Detecting and overcoming crystal twinning

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Between objectivity and subjectivity

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Improved Fourier coefficients for maps using phases from partial structures with errors

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Accurate bond and angle parameters for X-ray protein structure refinement

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

On the treatment of negative intensity observations

1 reference

https://api.crossref.org/works/10.1016%2FJ.STR.2011.08.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Identifiers

10.1016/J.STR.2011.08.006

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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