Journal of Molecular Biology

Article	Citations
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	311
Editorial Board	289
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	209
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	150
Outside Front Cover	137
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	119
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	115
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	109
HIV-Induced CPSF6 Condensates	107
Transcriptional and Epigenetic Regulation of Gasdermins	95
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	92
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	88
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	85
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	85
Intein-based Design Expands Diversity of Selenocysteine Reporters	83
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	81
Outside Front Cover	81
Outside Front Cover	77
Outside Front Cover	72
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	71
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	71
Outside Front Cover	63
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	62
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	60
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	59

Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	59
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	58
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	58
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	57
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	57
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	56
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	56
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	55
Mechanisms of Gasdermin Recognition by Proteases	55
Biomolecular Condensates as Novel Antiviral Targets	53
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	52
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	52
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	51
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	51
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	48
Pyroptosis, and its Role in Central Nervous System Disease	47
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	46
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	44
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	44
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	43
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	43
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	42
Extracellular uncoating of bacteriophage MS2	42
Mechanisms of Translation-coupled Quality Control	42
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	41
Chaperone Recycling in Late-Stage Flagellar Assembly	40
Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region	40
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	40
GMMA Can Stabilize Proteins Across Different Functional Constraints	40
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	39
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	39
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	38
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	38
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	38
Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry	37
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	37
Editorial Board	37
Outside Front Cover	36
Outside Front Cover	35
Editorial Board	35
Outside Front Cover	35
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	35
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement	34
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	34
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	34
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	34
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	34
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	33
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	33
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	32

R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	32
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	32
Near-Infrared Optogenetic Module for Conditional Protein Splicing	32
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	32
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	31
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	31
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	31
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	30
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	30
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	30
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator	30
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	30
GRAMMCell: Docking-based Cell Modeling Resource	29
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	29
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	29
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	29
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	29
Biosynthesis and Genetic Incorporation of 3,4-Dihydroxy-L-Phenylalanine into Proteins in Escherichia coli	29
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	29
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	28
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	28
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	28
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	28
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	28
Anthrax Toxin: Model System for Studying Protein Translocation	28
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	28
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	28
Editorial Board	28
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	27
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	27
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	27
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	27
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	27
The Role of LRRK2 in Intracellular Organelle Dynamics	27
Editorial Board	27
D154Q Mutation does not Alter KRAS Dimerization	27
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	26
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	26
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	26
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	26
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	26
Co-Translational Membrane Targeting and Holo-Translocon Docking of Ribosomes Translating the SRP Receptor	26
Structure of the Borrelia Bacteriophage φBB1 Procapsid	26
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	26
Gasdermin Pore Forming Activities that Promote Inflammation from Living and Dead Cells	26
The Evolution of Sequence Specificity in a DNA Binding Protein Family	26
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	26
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	26
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	26
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	25
memerna: Sparse RNA folding including coaxial stacking	25
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	25
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	25
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	24
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	24
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	24
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	24
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	24
Editorial Board	24
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	24
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	24
Corrigendum to “Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria” [J. Mol. Biol. 432(14) (2020) 4032–4048]	23
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	23
Outside Front Cover	23
Editorial Board	23
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	23
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	23
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	23
Global Analysis of Multi-Mutants to Improve Protein Function	23
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	23
Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B	23
Editorial Board	23
DeepMS: super-fast peptide identification using end-to-end deep learning method	22
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Inflammasomes in T cells	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	22
Insight into the Conformational Ensembles Formed by U–U and T–T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations	22
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	22

Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	22
Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action	22
Editorial Board	22
Structural Analysis of Mammalian Sialic Acid Esterase	22
Editorial Board	22
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	22
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	21
Editorial Board	21
Editorial Board	21
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	21
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	21
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	21
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus	21
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	21
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	21
Outside Front Cover	21
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	21
Epithelial Pyroptosis in Host Defense	21
Outside Front Cover	20
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	20
FTO Suppresses STAT3 Activation and Modulates Proinflammatory Interferon-Stimulated Gene Expression	20
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	20
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
K-Pro: Kinetics Data on Proteins and Mutants	20
Editorial Board	20
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	20
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	20
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	20
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	20
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	20
The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNASec Recognition and its Interactions	20
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	20
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	19
PANDA: PAN Cancer Data Analysis Web Tool	19
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	19
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
Unexpected Richness of the Bacterial Small RNA World	19
Editorial Board	19
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	19
Timing of TolA and TolQ Recruitment at the Septum Depends on the Functionality of the Tol-Pal System	19
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	19
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	19
Formation Mechanism and Antibacterial Activity of Natural Antimicrobial Lysozyme with Antibiotics Doxycycline and Tigecycline	19
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	19
Structural Dynamics of the C-terminal X Domain of Nipah and Hendra Viruses Controls the Attachment to the C-terminal Tail of the Nucleocapsid Protein	19
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	18
Outside Front Cover	18
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	18
Mitochondrial tRNA-specific Taurine Modifications Correlate With Ferroptosis-associated Myocardial Injury	18
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	18
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	18
Structural Dynamics of Rho GTPases	18
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	18
Evolution of temperature dependence of TRPM2 channel gating and inactivation in vertebrates	18
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	18
Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development	18
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	18
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	18
Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase	18
Outside Front Cover	18
Editorial Board	18
Channel Gating in Kalium Channelrhodopsin Slow Mutants	17
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	17
Outside Front Cover	17
Corrigendum to “Novel LRR-ROC Motif That Links the N- and C-terminal Domains in LRRK2 Undergoes an Order–Disorder Transition Upon Activation” [J. Mol. Biol. 435(12) (2023) 1–17]	17
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	17
Charge Segregation in the Intrinsically Disordered Region Governs VRN1 and DNA Liquid-like Phase Separation Robustness	17
Signal Propagation Within the MCL-1/BIM Protein Complex	17
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
Outside Front Cover	17
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	17
Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future	17
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	17
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain	17
In Silico Approaches for Prediction of Anti-CRISPR Proteins	17
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	17
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	17
The Interplay Between Disordered Regions in RNAs and Proteins Modulates Interactions Within Stress Granules and Processing Bodies	17
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	17
An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA	16
The Protein Scaffolding Functions of Polyphosphate	16
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	16
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	16
The Functional Relationship Between RNA Splicing and the Chromatin Landscape	16
Sequence Determinants of Allosteric Back-to-front Control of the Arf Nucleotide Switch	16
Applications of Genetic Code Expansion in Studying Protein Post-translational Modification	16
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	16
From embryos to condensates: A developmental biologist’s journey	16
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	16