Real-space refinement in PHENIX for cryo-EM and crystallography (Q54691589)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29872004%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

title

Real-space refinement in PHENIX for cryo-EM and crystallography (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29872004%20AND%20SRC:MED&resulttype=core&format=json

cryogenic electron microscopy

30 March 2020

main subject

0 references

1 reference

1

1 reference

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30 March 2020

Billy K Poon

2

1 reference

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30 March 2020

Randy Read

3

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30 March 2020

Paul D. Adams

7

1 reference

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30 March 2020

6

Alexandre Urzhumtsev

1 reference

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30 March 2020

author name string

Oleg V Sobolev

4

1 reference

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30 March 2020

Thomas C Terwilliger

5

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30 March 2020

publication date

30 May 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29872004%20AND%20SRC:MED&resulttype=core&format=json

Acta crystallographica. Section D, Structural biology

30 March 2020

published in

1 reference

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30 March 2020

volume

74

1 reference

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30 March 2020

issue

Pt 6

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30 March 2020

page(s)

531-544

1 reference

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Validation of Structures in the Protein Data Bank

30 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

MolProbity: More and better reference data for improved all-atom structure validation

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Tools for the Cryo-EM Gold Rush: Going from the cryo-EM map to the atomistic model

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

`Atomic resolution': a badly abused term in structural biology.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Accurate model annotation of a near-atomic resolution cryo-EM map.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Cryo-EM structure of the large subunit of the spinach chloroplast ribosome

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Structure of the STRA6 receptor for retinol uptake

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Programming new geometry restraints: parallelity of atomic groups

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Metrics for comparison of crystallographic maps

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Model morphing and sequence assignment after molecular replacement

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

MAIN software for density averaging, model building, structure refinement and validation.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Statistical quality indicators for electron-density maps

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Towards automated crystallographic structure refinement with phenix.refine

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Outcome of the first electron microscopy validation task force meeting

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Features and development of Coot

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

MolProbity: all-atom structure validation for macromolecular crystallography

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Automatic multiple-zone rigid-body refinement with a large convergence radius

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

SHELXL: high-resolution refinement

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Crystallographic R factor refinement by molecular dynamics

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Automated protein-ligand crystallography for structure-based drug design

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Introduction to macromolecular refinement

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Coot: model-building tools for molecular graphics

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Likelihood-based refinement. I. Irremovable model errors.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Fitting atomic models into electron-microscopy maps

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6096492

Combining Electron Microscopic with X-Ray Crystallographic Structures

7 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29872004

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Automated map sharpening by maximization of detail and connectivity.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29872004

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S2059798318006551

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29872004%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29872004%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

PubMed publication ID

29872004

1 reference