Real-space refinement in PHENIX for cryo-EM and crystallography

scientific article published on 30 May 2018

Real-space refinement in PHENIX for cryo-EM and crystallography is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1107/S2059798318006551
P932PMC publication ID6096492
P698PubMed publication ID29872004

P50authorRandy ReadQ18011401
Pavel V AfonineQ89000648
Billy K PoonQ89000652
Alexandre UrzhumtsevQ96607292
Paul D. AdamsQ30504798
P2093author name stringThomas C Terwilliger
Oleg V Sobolev
P2860cites workA new generation of crystallographic validation tools for the protein data bankQ24634970
KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization programQ24646196
MolProbity: all-atom structure validation for macromolecular crystallographyQ24649111
PHENIX: a comprehensive Python-based system for macromolecular structure solutionQ24654617
Improved methods for building protein models in electron density maps and the location of errors in these modelsQ26776980
Crystallography & NMR System: A New Software Suite for Macromolecular Structure DeterminationQ26778405
3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EMQ27322840
Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA cappingQ27666544
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modelingQ27679009
Structure of the TRPV1 ion channel determined by electron cryo-microscopyQ27680759
Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EMQ27698054
2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite LeishmaniaQ27715930
Structure of the STRA6 receptor for retinol uptakeQ27727740
Coot: model-building tools for molecular graphicsQ27860505
Towards automated crystallographic structure refinement with phenix.refineQ27860678
Free R value: a novel statistical quantity for assessing the accuracy of crystal structuresQ27860894
Validation of Structures in the Protein Data BankQ46645138
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translationQ49785061
Likelihood-based refinement. I. Irremovable model errorsQ52042540
A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solventQ52069647
`Atomic resolution': a badly abused term in structural biology.Q54864712
Combining Electron Microscopic with X-Ray Crystallographic StructuresQ63866208
Automated map sharpening by maximization of detail and connectivity.Q64937611
SHELXL: high-resolution refinementQ27860933
Crystallographic R factor refinement by molecular dynamicsQ27860942
The Protein Data Bank: a computer-based archival file for macromolecular structuresQ27860989
Features and development of CootQ27861079
EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural informationQ28187834
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid actionQ28574929
Outcome of the first electron microscopy validation task force meetingQ28730539
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinementQ30300619
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.Q30674904
Cryo-EM structure of the large subunit of the spinach chloroplast ribosomeQ30824910
4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1Q30833513
Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturationQ30837348
Accurate model annotation of a near-atomic resolution cryo-EM map.Q30843351
Automated protein-ligand crystallography for structure-based drug designQ33253602
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinementQ33582475
Metrics for comparison of crystallographic mapsQ34299253
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolutionQ35878822
Programming new geometry restraints: parallelity of atomic groupsQ35903383
Introduction to macromolecular refinementQ35968233
EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.Q36109022
Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.Q36419241
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular modelsQ36790438
Automatic multiple-zone rigid-body refinement with a large convergence radiusQ37267251
Model morphing and sequence assignment after molecular replacementQ37280214
UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis.Q38677893
Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 BacteriophageQ38739686
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.Q38759268
CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen InterfaceQ40200645
Tools for the Cryo-EM Gold Rush: Going from the cryo-EM map to the atomistic modelQ41596210
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructionsQ41606440
Fitting atomic models into electron-microscopy mapsQ41631474
MAIN software for density averaging, model building, structure refinement and validation.Q42156127
Statistical quality indicators for electron-density mapsQ42552365
MolProbity: More and better reference data for improved all-atom structure validationQ42695568
P433issuePt 6
P921main subjectcrystallographyQ160398
cryogenic electron microscopyQ5190506
P304page(s)531-544
P577publication date2018-05-30
P1433published inActa crystallographica. Section D, Structural biologyQ27727181
P1476titleReal-space refinement in PHENIX for cryo-EM and crystallography
P478volume74

Reverse relations

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