(Q30857678)

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Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

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scholarly article

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Europe PubMed Central

17 October 2017

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data (English)

1 reference

Europe PubMed Central

17 October 2017

macromolecular structure

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1 reference

based on heuristic

inferred from title

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Thomas C. Terwilliger

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object named as

Thomas C Terwilliger

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Europe PubMed Central

17 October 2017

language of work or name

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based on heuristic

inferred from title

publication date

30 September 2014

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Europe PubMed Central

17 October 2017

Acta Crystallographica Section D: Biological Crystallography

1 reference

Europe PubMed Central

17 October 2017

70

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Europe PubMed Central

17 October 2017

Pt 10

1 reference

Europe PubMed Central

17 October 2017

2533-2543

1 reference

Europe PubMed Central

17 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Bulk-solvent and overall scaling revisited: faster calculations, improved results

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Visualizing ligand molecules in Twilight electron density

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

On the variability of experimental data in macromolecular crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

PDB_REDO: constructive validation, more than just looking for errors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Implementing an X-ray validation pipeline for 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=4188001

21 June 2018

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Completion of autobuilt protein models using a database of protein fragments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Automatic rebuilding and optimization of crystallographic structures in 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=4188001

21 June 2018

A new generation of crystallographic validation tools for 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=4188001

21 June 2018

Reduction of density-modification bias by β correction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Overview of the CCP4 suite and current developments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Features and development of Coot

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Recent developments in classical density modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Diffraction data analysis in the presence of radiation damage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Averaged kick maps: less noise, more signal... and probably less bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Lessons from structural genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Alternative models for two crystal structures of bovine rhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Exploiting the anisotropy of anomalous scattering boosts the phasing power of SAD and MAD experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Surprises and pitfalls arising from (pseudo)symmetry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Quality 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=4188001

21 June 2018

An alternate description of two crystal structures of phospholipase A2 from Bungarus caeruleus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

The Buccaneer software for automated model building. 1. Tracing protein chains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 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=4188001

21 June 2018

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=4188001

21 June 2018

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=4188001

21 June 2018

Maximum-likelihood density modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Crystal structures of myoglobin-ligand complexes at near-atomic resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Remarks about protein structure precision

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

Crystallographic data deposition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

21 June 2018

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=4188001

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

25 November 2018

Multivariate phase combination improves automated crystallographic model building.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

25 November 2018

Using prime-and-switch phasing to reduce model bias in molecular replacement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

25 November 2018

Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model bias.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188001

25 November 2018

Flat bulk-solvent model: obtaining optimal parameters

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286839

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Is one solution good enough?

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286839

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Detection and correction of underassigned rotational symmetry prior to structure deposition

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286839

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Towards automated crystallographic structure refinement with phenix.refine

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286839

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Why are protein crystallographic R-values so high?

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286839

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1107/S1399004714017040

1 reference

Europe PubMed Central

17 October 2017

release_5zlmn5adnvd2jbn5ly7467ztwi

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https://api.fatcat.wiki/v0/release/5zlmn5adnvd2jbn5ly7467ztwi

24 November 2022

based on heuristic

mapped directly with Wikidata item

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Europe PubMed Central

17 October 2017

1 reference

Europe PubMed Central

17 October 2017

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