Acta Crystallographica Section D-Structural Biology

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
CCP4 Cloud for structure determination and project management in macromolecular crystallography	33
xia2.multiplex: a multi-crystal data-analysis pipeline	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
Improving sampling of crystallographic disorder in ensemble refinement	25
Accelerating crystal structure determination with iterative AlphaFold prediction	25
Optimized cryo-EM data-acquisition workflow by sample-thickness determination	25
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300	23
The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting	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
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
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
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
Molecular-dynamics simulation methods for macromolecular crystallography	16
Validation, analysis and annotation of cryo-EM structures	16
Substrate binding in the bile acid transporter ASBTYffromYersinia 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
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
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
The missing link: covalent linkages in structural models	14
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
Low-resolution structures of modular nanotransporters shed light on their functional activity	13
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
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
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
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	11
Phasertng: directed acyclic graphs for crystallographic phasing	11
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
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
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
Real-space quantum-based refinement for cryo-EM: Q|R#3	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
Recent structural insights into the mechanism of lysozyme hydrolysis	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
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
Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership	9
Crystal structure of fungal tannase from Aspergillus niger	9
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
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
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
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa	6
Analysis and validation of overall N-glycan conformation in Privateer	6
Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase	6
Errors in structural biology are not the exception	6
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	6
Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3	6
Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea	6
Over the rainbow: structural characterization of the chromoproteins gfasPurple, amilCP, spisPink and eforRed	6
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons	6
Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase	6
Crystal structures of adenylylated and unadenylylated PIIprotein GlnK fromCorynebacterium glutamicum	6
Development of CryoVR, a virtual reality training system for hands-on cryoEM operations	6
Databases for intrinsically disordered proteins	6
A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs	6
Ab initio determination of the shape of membrane proteins in a nanodisc	6
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum	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
Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase	6
Room-temperature serial synchrotron crystallography of Drosophila cryptochrome	6
Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank	6
Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development	6
Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties	5
Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center	5
Real space in cryo-EM: the future is local	5
The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2	5
Detection of translational noncrystallographic symmetry in Patterson functions	5
Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells	5
Correcting systematic errors in diffraction data with modern scaling algorithms	5
Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii	5
Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6	5
Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode	5
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands	5
Exiting the tunnel of uncertainty: crystal soak to validated hit	5
Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin	5
Crystal structure of a covalently linked Aurora-A–MYCN complex	5
The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2	5
A scalable strategy to solve structures of PDZ domains and their complexes	5

Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina	5
LAHMA: structure analysis through local annotation of homology-matched amino acids	5
Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites	5
Structural analysis of the sulfatase AmAS from Akkermansia muciniphila	5
Ten things I `hate' about refinement	5
Development and assessment of CootVR, a virtual reality computer program for model building	5
A rush to explore protein–ligand electrostatic interaction energy with Charger	5
Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family	5
Radiation-induced defects in protein crystals observed by X-ray topography	5
The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme	5
Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021	4
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks	4
Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis	4
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model	4
Structure and mechanism of the γ-glutamyl-γ-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa	4
Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap	4
Structure of human factor VIIa–soluble tissue factor with calcium, magnesium and rubidium	4
Exploring ligand dynamics in protein crystal structures with ensemble refinement	4
Data collection from crystals grown in microfluidic droplets	4
Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase	4
End-to-end orientation estimation from 2D cryo-EM images	4
Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus	4
Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure	4
Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae	4
Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design	4
Crystal structures of β-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies	4
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography	4
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps	4
The LH–DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders	4
AlphaFold and the future of structural biology	4
Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis	4
Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs	4
Structural insight into the hydrolase and synthase activities of an alkaline α-galactosidase fromArabidopsisfrom complexes with substrate/product	4
Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity	4
2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data	4
Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein	4
Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2	3
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM	3
Structural and functional analysis of the D-alanyl carrier protein ligase DltA from Staphylococcus aureus Mu50	3
Integrated, rational molecular replacement	3
The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity	3
3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived α-ketoamide inhibitor	3
Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116	3
Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation–π interaction	3
Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER	3
Structural and functional investigation of a fungal member of carbohydrate esterase family 15 with potential specificity for rare xylans	3
The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complex	3
The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography	3
Detecting ice artefacts in processed macromolecular diffraction data with machine learning	3
A web-based dashboard for RELION metadata visualization	3
Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis	3
The TR-icOS setup at the ESRF: time-resolved microsecond UV–Vis absorption spectroscopy on protein crystals	3
Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution	3
Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program	3
Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy	3
LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments	3
Introduction to molecular replacement: a time perspective	3
Overall protein structure quality assessment using hydrogen-bonding parameters	3
K-edge anomalous SAXS for protein solution structure modeling	3
Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase	3
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7	3
Catalytically active holoHomo sapiensadenosine deaminase I adopts a closed conformation	3
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology	3
Structural basis of human LRG1 recognition by Magacizumab, a humanized monoclonal antibody with therapeutic potential	3
Theoretical and practical approaches to improve the performance of local correlation algorithms for volume data analysis and shape recognition	3
Predicting the performance of automated crystallographic model-building pipelines	3
Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam	3
Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations	3
Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis	3
The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family	3
Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures	3
Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius	3
Raw diffraction data are our ground truth from which all subsequent workflows develop	3
An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter	3
Crystal structure of DNA polymerase I from Thermus phage G20c	3
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	3
Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets	3
High-performance macromolecular data delivery and visualization for the web	3
Crystallization, structural characterization and kinetic analysis of a GH26 β-mannanase from Klebsiella oxytoca KUB-CW2-3	3
Crystal structures of UDP-N-acetylmuramic acid L-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine	3
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	3