(Q41606440)

5 October 2017

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

1 reference

cryogenic electron microscopy

5 October 2017

0 references

1 reference

Robert A Nicholls

3

0 references

Alan Brown

object named as

Alan Brown

1

0 references

author name string

Fei Long

2

1 reference

5 October 2017

Jaan Toots

4

1 reference

5 October 2017

Paul Emsley

5

1 reference

5 October 2017

Garib Murshudov

6

1 reference

5 October 2017

1 January 2015

1 reference

Acta Crystallographica Section D: Biological Crystallography

5 October 2017

1 reference

5 October 2017

71

1 reference

5 October 2017

Pt 1

1 reference

5 October 2017

136-153

1 reference

Collaborative computational project for electron cryo-microscopy.

5 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Conformation-independent structural comparison of macromolecules with ProSMART

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Beam-induced motion correction for sub-megadalton cryo-EM particles.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Finding the right fit: chiseling structures out of cryo-electron microscopy maps

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Structure of the Yeast Mitochondrial Large Ribosomal Subunit

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Atomic model of the F 420 -reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Cross-validation in cryo-EM-based structural modeling

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Cryo-EM model validation using independent map reconstructions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

RELION: implementation of a Bayesian approach to cryo-EM structure determination

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

RCrane: semi-automated RNA model building

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Prevention of overfitting in cryo-EM structure determination

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Real-space refinement with DireX: from global fitting to side-chain improvements.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Handling ligands with Coot

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Low-resolution refinement tools in REFMAC5.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Outcome of the first electron microscopy validation task force meeting

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Electronic detectors for electron microscopy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

REFMAC5 for the refinement of macromolecular crystal structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Overview of the CCP4 suite and current developments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

EMDataBank.org: unified data resource for CryoEM

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Dali server: conservation mapping in 3D

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Features and development of Coot

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Conformational change of flagellin for polymorphic supercoiling of the flagellar filament

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Molecular replacement with MOLREP

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

MolProbity: all-atom structure validation for macromolecular crystallography

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

An automated procedure for detecting protein folds from sub-nanometer resolution electron density

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Refinement of protein structures into low-resolution density maps using rosetta

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

BPS: a database of RNA base-pair structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Structural basis for translation termination on the 70S ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

BALBES: a molecular-replacement pipeline

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Identification of secondary structure elements in intermediate-resolution density maps

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Coot: model-building tools for molecular graphics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Potential use of real-space refinement in protein structure determination.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

UCSF Chimera--a visualization system for exploratory research and analysis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy

6 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

6 June 2018

https://pubmed.ncbi.nlm.nih.gov/25615868

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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=4304694

The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Structure of the carboxypeptidase Y inhibitor IC in complex with the cognate proteinase reveals a novel mode of the proteinase-protein inhibitor interaction

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

An approach to examining model dependence in EM reconstructions using cross-validation

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

PDP: protein domain parser.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304694

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

19 August 2018

1 reference

https://api.crossref.org/works/10.1107%2FS1399004714021683

Quantifying the local resolution of cryo-EM density maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS1399004714021683

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS1399004714021683

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS1399004714021683

The Resolution Revolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS1399004714021683

Structural biology. Beyond blob-ology

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25615868

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S1399004714021683

1 reference

5 October 2017

1 reference

5 October 2017

PubMed publication ID

25615868

1 reference