OOIR: Observatory of International Research

Papers

(The TQCC of Acta Crystallographica Section D-Structural Biology is 7. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)

Article	Citations
The CCP4 suite: integrative software for macromolecular crystallography	225
Cryo-EM single-particle structure refinement and map calculation usingServalcat	159
Implications of AlphaFold2 for crystallographic phasing by molecular replacement	72
Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162	69
Using photocaging for fast time-resolved structural biology studies	44
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE	42
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?	38
xia2.multiplex: a multi-crystal data-analysis pipeline	33
CCP4 Cloud for structure determination and project management in macromolecular crystallography	33
TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows	32
Best practices for time-resolved serial synchrotron crystallography	30
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report	29
eSPC: an online data-analysis platform for molecular biophysics	28
New system for archiving integrative structures	27
Structural dynamics: review of time-resolved cryo-EM	26
Accelerating crystal structure determination with iterative AlphaFold prediction	25
Optimized cryo-EM data-acquisition workflow by sample-thickness determination	25
Improving sampling of crystallographic disorder in ensemble refinement	25
The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting	23
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300	23
Adaptive Cartesian and torsional restraints for interactive model rebuilding	22
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	20
ModelCraft: an advanced automated model-building pipeline using Buccaneer	18
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition	18
On-grid and in-flow mixing for time-resolved cryo-EM	18

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion	18
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking	17
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments	17
Substrate binding in the bile acid transporter ASBT_YffromYersinia frederiksenii	16
Homogeneous batch micro-crystallization of proteins from ammonium sulfate	16
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	16
Molecular-dynamics simulation methods for macromolecular crystallography	16
Validation, analysis and annotation of cryo-EM structures	16
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models	15
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP	15
Validation analysis of EMDB entries	15
A new inactive conformation of SARS-CoV-2 main protease	15
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization	15
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins	14
Fast fragment- and compound-screening pipeline at the Swiss Light Source	14
Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR	14
The missing link: covalent linkages in structural models	14
Modelling covalent linkages in CCP4	13
Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex	13
Low-resolution structures of modular nanotransporters shed light on their functional activity	13
Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1	12
B-factor accuracy in protein crystal structures	12
Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography	12
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	12
Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking	12
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals	12
FLEXR: automated multi-conformer model building using electron-density map sampling	12
The structure of natively iodinated bovine thyroglobulin	12
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	12
Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography	12
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	12
Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid	12
A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides	12
Crystal structure of the middle and C-terminal domains of Hsp90α labeled with a coumarin derivative reveals a potential allosteric binding site as a drug target	11
Identification of Mg²⁺ ions next to nucleotides in cryo-EM maps using electrostatic potential maps	11
High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system	11
Sequence-assignment validation in cryo-EM models with checkMySequence	11
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain	11
Shift-field refinement of macromolecular atomic models	11
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	11
Phasertng: directed acyclic graphs for crystallographic phasing	11
High-resolution structure determination using high-throughput electron cryo-tomography	10
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0	10
Likelihood-based docking of models into cryo-EM maps	10
Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre	10
Principal component analysis is limited to low-resolution analysis in cryoEM	10
Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states	10
A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip	10
Macromolecular crystallography using microcrystal electron diffraction	10
Recent structural insights into the mechanism of lysozyme hydrolysis	9

STOPGAP: an open-source package for template matching, subtomogram alignment and classification	9
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching	9
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	9
Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion	9
20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening	9
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus	9
New restraints and validation approaches for nucleic acid structures in PDB-REDO	9
Crystal structure of fungal tannase from Aspergillus niger	9
Real-space quantum-based refinement for cryo-EM: Q\|R#3	9
Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership	9
Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies	9
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system	9
Arginine off-kilter: guanidinium is not as planar as restraints denote	9
Native SAD phasing at room temperature	9
The structure of Prp2 bound to RNA and ADP-BeF₃⁻reveals structural features important for RNA unwinding by DEAH-box ATPases	9
In situ ligand restraints from quantum-mechanical methods	8
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned	8
Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score	8
HomogeneouslyN-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis	8
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	8
Using deep-learning predictions of inter-residue distances for model validation	8
Ice in biomolecular cryocrystallography	8
Structural biology of coronavirus ion channels	8
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	8
AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals	8
GEMMI and Servalcat restrain REFMAC5	8
Updated restraint dictionaries for carbohydrates in the pyranose form	8
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae	8
Determining the oxidation state of elements by X-ray crystallography	7
Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF	7
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature	7
Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method	7
How do I get the most out of my protein sequence using bioinformatics tools?	7
A case for glycerol as an acceptable additive for single-particle cryoEM samples	7
Predicted models and CCP4	7
Atomic model validation using the CCP-EM software suite	7
Near-atomic resolution reconstructions from in situ revitrified cryo samples	7
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization	7
Versatile microporous polymer-based supports for serial macromolecular crystallography	7
Crystal structure of a novel homodimericD-allulose 3-epimerase from a Clostridia bacterium	7
Using RELION software within the Scipion framework	7
Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin	7