OOIR: Observatory of International Research

Papers

(The TQCC of Acta Crystallographica Section D-Structural Biology is 6. 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 2020-05-01 to 2024-05-01.)

Article	Citations
The CCP4 suite: integrative software for macromolecular crystallography	127
Cryo-EM single-particle structure refinement and map calculation usingServalcat	125
Implications of AlphaFold2 for crystallographic phasing by molecular replacement	67
Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162	60
Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER	47
Combining high throughput and high quality for cryo-electron microscopy data collection	44
Using photocaging for fast time-resolved structural biology studies	42
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?	33
Through-grid wicking enables high-speed cryoEM specimen preparation	31
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE	31
TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows	31
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM	30
Density modification of cryo-EM maps	29
FragMAX: the fragment-screening platform at the MAX IV Laboratory	27
eSPC: an online data-analysis platform for molecular biophysics	26
xia2.multiplex: a multi-crystal data-analysis pipeline	26
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report	24
Crystal structures of human ENPP1 in apo and bound forms	24
Optimized cryo-EM data-acquisition workflow by sample-thickness determination	23
Best practices for time-resolved serial synchrotron crystallography	23
CCP4 Cloud for structure determination and project management in macromolecular crystallography	23
New system for archiving integrative structures	22
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300	21
The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting	20
Improving sampling of crystallographic disorder in ensemble refinement	20

Adaptive Cartesian and torsional restraints for interactive model rebuilding	19
Accelerating crystal structure determination with iterative AlphaFold prediction	19
Structural dynamics: review of time-resolved cryo-EM	18
Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis	18
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion	18
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	17
Predicting protein model correctness in Coot using machine learning	17
Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods	16
Substrate binding in the bile acid transporter ASBT_YffromYersinia frederiksenii	16
On-grid and in-flow mixing for time-resolved cryo-EM	16
Validation, analysis and annotation of cryo-EM structures	15
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition	15
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments	15
Homogeneous batch micro-crystallization of proteins from ammonium sulfate	14
Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR	14
ModelCraft: an advanced automated model-building pipeline using Buccaneer	14
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models	14
Molecular-dynamics simulation methods for macromolecular crystallography	14
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
A new inactive conformation of SARS-CoV-2 main protease	13
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP	13
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking	13
Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly	12
Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1	12
Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org	12
Crown-ether-mediated crystal structures of the glycosyltransferasePaGT3 fromPhytolacca americana	12
Fast fragment- and compound-screening pipeline at the Swiss Light Source	12
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	12
Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER	12
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	12
Targeting the innate immune receptor TLR8 using small-molecule agents	12
Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking	11
The missing link: covalent linkages in structural models	11
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	11
The structure of natively iodinated bovine thyroglobulin	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
Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis	11
Validation analysis of EMDB entries	11
B-factor accuracy in protein crystal structures	11
Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography	10
A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides	10
Local and global analysis of macromolecular atomic displacement parameters	10
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization	10
Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states	10
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain	10
Principal component analysis is limited to low-resolution analysis in cryoEM	10
Shift-field refinement of macromolecular atomic models	10
Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid	10
Identification of Mg²⁺ ions next to nucleotides in cryo-EM maps using electrostatic potential maps	10

Phasertng: directed acyclic graphs for crystallographic phasing	10
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins	10
Modelling covalent linkages in CCP4	10
A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip	9
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	9
Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography	9
Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips	9
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	9
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals	9
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	9
The RING domain of TRIM69 promotes higher-order assembly	9
Macromolecular crystallography using microcrystal electron diffraction	9
The structure of Prp2 bound to RNA and ADP-BeF₃⁻reveals structural features important for RNA unwinding by DEAH-box ATPases	9
Recent structural insights into the mechanism of lysozyme hydrolysis	9
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system	9
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching	9
Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies	8
Ice in biomolecular cryocrystallography	8
HomogeneouslyN-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis	8
Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel	8
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0	8
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus	8
Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi	8
Native SAD phasing at room temperature	8
Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion	8
Structural biology of coronavirus ion channels	8
Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin	8
How do I get the most out of my protein sequence using bioinformatics tools?	7
Versatile microporous polymer-based supports for serial macromolecular crystallography	7
Atomic model validation using the CCP-EM software suite	7
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae	7
Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin	7
Arginine off-kilter: guanidinium is not as planar as restraints denote	7
Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre	7
Real-space quantum-based refinement for cryo-EM: Q\|R#3	7
Using RELION software within the Scipion framework	7
Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples	7
A solution-free crystal-mounting platform for native SAD	7
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	7
High-resolution structure determination using high-throughput electron cryo-tomography	7
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature	7
Updated restraint dictionaries for carbohydrates in the pyranose form	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
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	7
Structural and biochemical characterization of novel carbonic anhydrases fromPhaeodactylum tricornutum	6
Crystal structure of fungal tannase from Aspergillus niger	6
Structure–functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands	6
C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening	6
Real space in cryo-EM: the future is local	6
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization	6
Using deep-learning predictions of inter-residue distances for model validation	6
High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor	6
Ab initio determination of the shape of membrane proteins in a nanodisc	6
Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase	6
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	6
Likelihood-based docking of models into cryo-EM maps	6
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands	6
FLEXR: automated multi-conformer model building using electron-density map sampling	6
High-throughput in situ experimental phasing	6
Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development	6
Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties	6
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa	6
New restraints and validation approaches for nucleic acid structures in PDB-REDO	6
Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea	6
Sequence-assignment validation in cryo-EM models with checkMySequence	6
In situ ligand restraints from quantum-mechanical methods	6