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 2020-04-01 to 2024-04-01.)

Article	Citations
Cryo-EM single-particle structure refinement and map calculation usingServalcat	118
The CCP4 suite: integrative software for macromolecular crystallography	115
Implications of AlphaFold2 for crystallographic phasing by molecular replacement	64
Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162	56
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	40
Using photocaging for fast time-resolved structural biology studies	39
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	30
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM	30
Density modification of cryo-EM maps	28
FragMAX: the fragment-screening platform at the MAX IV Laboratory	26
xia2.multiplex: a multi-crystal data-analysis pipeline	25
Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions	24
Crystal structures of human ENPP1 in apo and bound forms	24
eSPC: an online data-analysis platform for molecular biophysics	24
Best practices for time-resolved serial synchrotron crystallography	23
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report	23
Industrial cryo-EM facility setup and management	21
New system for archiving integrative structures	21
CCP4 Cloud for structure determination and project management in macromolecular crystallography	21
Optimized cryo-EM data-acquisition workflow by sample-thickness determination	21
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300	20

Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis	18
Structural dynamics: review of time-resolved cryo-EM	18
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion	18
Accelerating crystal structure determination with iterative AlphaFold prediction	18
Predicting protein model correctness in Coot using machine learning	17
Improving sampling of crystallographic disorder in ensemble refinement	17
The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting	16
Adaptive Cartesian and torsional restraints for interactive model rebuilding	16
Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods	16
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	16
On-grid and in-flow mixing for time-resolved cryo-EM	15
Validation, analysis and annotation of cryo-EM structures	14
Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR	14
Homogeneous batch micro-crystallization of proteins from ammonium sulfate	14
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking	13
Substrate binding in the bile acid transporter ASBT_YffromYersinia frederiksenii	13
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models	13
ModelCraft: an advanced automated model-building pipeline using Buccaneer	13
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP	13
A new inactive conformation of SARS-CoV-2 main protease	13
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition	13
Targeting the innate immune receptor TLR8 using small-molecule agents	12
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
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	12
Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex	12
Crown-ether-mediated crystal structures of the glycosyltransferasePaGT3 fromPhytolacca americana	12
Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org	12
Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER	12
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments	12
Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis	11
Fast fragment- and compound-screening pipeline at the Swiss Light Source	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
Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking	11
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	11
B-factor accuracy in protein crystal structures	11
Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states	10
Low-resolution structures of modular nanotransporters shed light on their functional activity	10
Principal component analysis is limited to low-resolution analysis in cryoEM	10
Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins	10
Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid	10
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site	10
The missing link: covalent linkages in structural models	10
Shift-field refinement of macromolecular atomic models	10
Modelling covalent linkages in CCP4	10
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
Phasertng: directed acyclic graphs for crystallographic phasing	10
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization	10

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
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	9
Molecular-dynamics simulation methods for macromolecular crystallography	9
Local and global analysis of macromolecular atomic displacement parameters	9
A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip	9
The RING domain of TRIM69 promotes higher-order assembly	9
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching	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
Identification of Mg²⁺ ions next to nucleotides in cryo-EM maps using electrostatic potential maps	9
Crystal and solution structures of fragments of the human leucocyte common antigen-related protein	9
Ion permeation in potassium ion channels	9
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system	9
Macromolecular crystallography using microcrystal electron diffraction	9
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	9
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	9
Validation analysis of EMDB entries	9
The structure of Prp2 bound to RNA and ADP-BeF₃⁻reveals structural features important for RNA unwinding by DEAH-box ATPases	9
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals	9
Native SAD phasing at room temperature	8
Ice in biomolecular cryocrystallography	8
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins	8
Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi	8
Recent structural insights into the mechanism of lysozyme hydrolysis	8
Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies	8
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus	8
HomogeneouslyN-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis	8
Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin	8
Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion	8
Structural biology of coronavirus ion channels	8
Structural and thermodynamic analyses of interactions between death-associated protein kinase 1 and anthraquinones	8
Arginine off-kilter: guanidinium is not as planar as restraints denote	7
Versatile microporous polymer-based supports for serial macromolecular crystallography	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
How do I get the most out of my protein sequence using bioinformatics tools?	7
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain	7
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature	7
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae	7
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	7
Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre	7
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0	7
Atomic model validation using the CCP-EM software suite	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
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization	6
High-throughput in situ experimental phasing	6
Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel	6
Crystal structure of fungal tannase from Aspergillus niger	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
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	6
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands	6
Likelihood-based docking of models into cryo-EM maps	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
Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties	6
Structure–functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands	6
New restraints and validation approaches for nucleic acid structures in PDB-REDO	6
Sequence-assignment validation in cryo-EM models with checkMySequence	6
High-resolution structure determination using high-throughput electron cryo-tomography	6
Structural and biochemical characterization of novel carbonic anhydrases fromPhaeodactylum tricornutum	6
Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development	6
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa	6
Updated restraint dictionaries for carbohydrates in the pyranose form	6
Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin	6
Real space in cryo-EM: the future is local	6