(Q90549021)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31588918%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

review article

1 reference

title

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (English)

1 reference

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14 April 2020

1

1 reference

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14 April 2020

Pavel V Afonine

2

1 reference

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14 April 2020

Bradley J Hintze

7

1 reference

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14 April 2020

Li-Wei Hung

8

1 reference

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14 April 2020

Nigel W Moriarty

11

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14 April 2020

Robert Oeffner

12

1 reference

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14 April 2020

Billy K Poon

13

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14 April 2020

Randy Read

15

1 reference

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14 April 2020

Massimo Sammito

18

1 reference

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14 April 2020

Oleg V Sobolev

19

1 reference

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14 April 2020

Thomas C. Terwilliger

21

1 reference

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14 April 2020

Paul D. Adams

25

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14 April 2020

Jane Shelby Richardson

16

object named as

Jane S Richardson

1 reference

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14 April 2020

5

Vincent B Chen

1 reference

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14 April 2020

23

Lizbeth L Videau

1 reference

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14 April 2020

6

Tristan I Croll

1 reference

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14 April 2020

Christopher J Williams

24

object named as

Christopher J Williams

1 reference

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14 April 2020

17

David C Richardson

1 reference

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14 April 2020

4

Gábor Bunkóczi

1 reference

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14 April 2020

9

Swati Jain

1 reference

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14 April 2020

14

Michael G Prisant

1 reference

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14 April 2020

10

Airlie J McCoy

1 reference

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14 April 2020

20

Duncan H Stockwell

1 reference

14 April 2020

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31588918%20AND%20SRC:MED&resulttype=core&format=json

Matthew L Baker

3

1 reference

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14 April 2020

Alexandre G Urzhumtsev

22

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14 April 2020

publication date

2 October 2019

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Acta crystallographica. Section D, Structural biology

14 April 2020

number of pages

17

0 references

published in

1 reference

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14 April 2020

volume

75

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14 April 2020

issue

Pt 10

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14 April 2020

page(s)

861-877

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

14 April 2020

cites work

1 reference

12 December 2020

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

1 reference

12 December 2020

Where freedom is given, liberties are taken

1 reference

12 December 2020

Density modification in x-ray crystallography.

1 reference

12 December 2020

Checking your imagination: applications of the free R value

1 reference

12 December 2020

Detecting and overcoming crystal twinning

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Automated MAD and MIR structure solution

1 reference

12 December 2020

Maximum-likelihood density modification

1 reference

12 December 2020

Docking structures of domains into maps from cryo-electron microscopy using local correlation

1 reference

12 December 2020

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

1 reference

12 December 2020

Automated structure solution, density modification and model building

1 reference

12 December 2020

PHENIX: building new software for automated crystallographic structure determination

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Choice of data-collection parameters based on statistic modelling

1 reference

12 December 2020

A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis

1 reference

12 December 2020

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

1 reference

12 December 2020

Substructure search procedures for macromolecular structures

1 reference

12 December 2020

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

1 reference

12 December 2020

A robust bulk-solvent correction and anisotropic scaling procedure

1 reference

12 December 2020

Anomalous signal indicators in protein crystallography

1 reference

12 December 2020

Automated ligand fitting by core-fragment fitting and extension into density

1 reference

12 December 2020

An introduction to stereochemical restraints

1 reference

12 December 2020

Ligand identification using electron-density map correlations

1 reference

12 December 2020

Comparative X-Ray and Neutron Diffraction Study of Bonding Effects in s-Triazine

1 reference

12 December 2020

On macromolecular refinement at subatomic resolution with interatomic scatterers

1 reference

12 December 2020

An introduction to molecular replacement

1 reference

12 December 2020

A short history of SHELX

1 reference

12 December 2020

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

1 reference

12 December 2020

Fast procedure for reconstruction of full-atom protein models from reduced representations.

1 reference

12 December 2020

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

1 reference

12 December 2020

SHELXL: high-resolution refinement

1 reference

12 December 2020

Sharpening high resolution information in single particle electron cryomicroscopy

1 reference

12 December 2020

Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis

1 reference

12 December 2020

Low-barrier hydrogen bond in photoactive yellow protein

1 reference

12 December 2020

Crystallographic model quality at a glance

1 reference

12 December 2020

Phasercrystallographic software

1 reference

12 December 2020

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

1 reference

12 December 2020

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

1 reference

12 December 2020

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

1 reference

12 December 2020

Recent developments in phasing and structure refinement for macromolecular crystallography

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Conformation dependence of backbone geometry in proteins.

1 reference

12 December 2020

MolProbity: all-atom structure validation for macromolecular crystallography

1 reference

12 December 2020

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

1 reference

12 December 2020

Introduction to phasing

1 reference

12 December 2020

Features and development of Coot

1 reference

12 December 2020

A description of the instruments, samples, protocols, and analyses that belong to the growing field of cryo-EM

1 reference

12 December 2020

Resolution measures in molecular electron microscopy

1 reference

12 December 2020

Joint X-ray and neutron refinement with phenix.refine

1 reference

12 December 2020

Femtosecond X-ray protein nanocrystallography

1 reference

12 December 2020

Improvement of molecular-replacement models with Sculptor

1 reference

12 December 2020

Improved molecular replacement by density- and energy-guided protein structure optimization

1 reference

12 December 2020

Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking

1 reference

12 December 2020

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

1 reference

12 December 2020

Towards automated crystallographic structure refinement with phenix.refine

1 reference

12 December 2020

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

1 reference

12 December 2020

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

1 reference

12 December 2020

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

1 reference

12 December 2020

Modelling dynamics in protein crystal structures by ensemble refinement

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase.

1 reference

12 December 2020

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

1 reference

12 December 2020

Improved low-resolution crystallographic refinement with Phenix and Rosetta

1 reference

12 December 2020

Model morphing and sequence assignment after molecular replacement

1 reference

12 December 2020

Phaser.MRage: automated molecular replacement

1 reference

12 December 2020

Quantifying the local resolution of cryo-EM density maps

1 reference

12 December 2020

Ligand placement based on prior structures: the guided ligand-replacement method

1 reference

12 December 2020

Diffuse X-ray scattering to model protein motions

1 reference

12 December 2020

The Resolution Revolution

1 reference

12 December 2020

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

1 reference

12 December 2020

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.

1 reference

12 December 2020

Serial crystallography using synchrotron radiation

1 reference

12 December 2020

Metrics for comparison of crystallographic maps

1 reference

12 December 2020

How cryo-EM is revolutionizing structural biology

1 reference

12 December 2020

FEM: feature-enhanced map.

1 reference

12 December 2020

The rate of cis-trans conformation errors is increasing in low-resolution crystal structures.

1 reference

12 December 2020

Serial femtosecond crystallography: the first five years

1 reference

12 December 2020

Computational Methods for RNA Structure Validation and Improvement

1 reference

12 December 2020

Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions

1 reference

12 December 2020

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

1 reference

12 December 2020

Programming new geometry restraints: parallelity of atomic groups

1 reference

12 December 2020

Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate

1 reference

12 December 2020

A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

1 reference

12 December 2020

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.

1 reference

12 December 2020

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.

1 reference

12 December 2020

Molprobity's ultimate rotamer-library distributions for model validation

1 reference

12 December 2020

De Novo modeling in cryo-EM density maps with Pathwalking

1 reference

12 December 2020

On the interpretation of electron microscopic maps of biological macromolecules

1 reference

12 December 2020

An editor for the generation and customization of geometry restraints.

1 reference

12 December 2020

Serial crystallography at synchrotrons and X-ray lasers

1 reference

12 December 2020

Serial Synchrotron X-Ray Crystallography (SSX).

1 reference

12 December 2020

Many Ways to Derivatize Macromolecules and Their Crystals for Phasing

1 reference

12 December 2020

UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis.

1 reference

12 December 2020

Interactive comparison and remediation of collections of macromolecular structures.

1 reference

12 December 2020

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

1 reference

12 December 2020

Visualization of chemical modifications in the human 80S ribosome structure

1 reference

12 December 2020

Solving the scalability issue in quantum-based refinement: Q|R#1.

1 reference

12 December 2020

Bringing diffuse X-ray scattering into focus.

1 reference

12 December 2020

Model validation: local diagnosis, correction and when to quit.

1 reference

12 December 2020

On the application of the expected log-likelihood gain to decision making in molecular replacement.

1 reference

12 December 2020

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

1 reference

12 December 2020

Automated map sharpening by maximization of detail and connectivity.

1 reference

12 December 2020

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.

1 reference

12 December 2020

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition

1 reference

12 December 2020

Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale

1 reference

12 December 2020

MicroED: a versatile cryoEM method for structure determination

1 reference

12 December 2020

New tools for the analysis and validation of cryo-EM maps and atomic models

1 reference

12 December 2020

Rapid structure determination of microcrystalline molecular compounds using electron diffraction

1 reference

12 December 2020

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

1 reference

12 December 2020

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

1 reference

12 December 2020

The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination

1 reference

12 December 2020

Iron-sulfur clusters have no right angles

1 reference

12 December 2020

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

1 reference

12 December 2020

Matplotlib: A 2D Graphics Environment

1 reference

28 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1109/MCSE.2007.55

Identifiers

DOI

10.1107/S2059798319011471

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31588918%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31588918%20AND%20SRC:MED&resulttype=core&format=json

14 April 2020

1 reference