Journal of Molecular Biology

Article	Citations
Editorial Board	389
Outside Front Cover	187
Outside Front Cover	155
Outside Front Cover	136
Outside Front Cover	124
Outside Front Cover	106
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	98
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	98
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	96
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	95
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	89
Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae	85
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	83
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	82
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	80
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	73
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	70
HIV-Induced CPSF6 Condensates	68
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	67
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	66
The Structure of a Thermostable Phage’s Portal Vertex and Neck Complex Illuminates the Headful Maturation Mechanism	65
Editorial Board	63
Deeptosis: A Deep Learning-Based Platform for Label-Free Discrimination of Apoptosis and Pyroptosis from Brightfield Microscopy	60
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	60
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	57

ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	57
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	56
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	55
Pioneers: Glucose Sensing and Control of Health-span and Lifespan	53
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	53
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	52
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	51
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	51
Mechanisms of Translation-coupled Quality Control	49
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	48
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	46
Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae	46
Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2	45
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	45
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	44
Extracellular uncoating of bacteriophage MS2	43
ABSEIL: A polypeptide helicity and ensemble prediction tool	43
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	43
Cell Lines CoCoPUTs: A Database of Codon and Codon-pair Usage Frequencies in Cell Lines	43
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	42
Biomolecular Condensates as Novel Antiviral Targets	42
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	41
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	41
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	40
Outside Front Cover	39
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	39
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	39
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	39
Rising Star: G Protein-coupled Receptors (GPCRs) in Microenvironment Pharmacology and Sensory Perception Pharmacology	39
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	38
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	37
Editorial Board	37
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	37
Outside Front Cover	37
Outside Front Cover	37
Outside Front Cover	37
Editorial Board	37
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	36
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	36
Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis	36
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	35
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	35
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	35
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	34
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	34
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	34
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	34
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	34
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	33
RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces	33

GMMA Can Stabilize Proteins Across Different Functional Constraints	33
Near-Infrared Optogenetic Module for Conditional Protein Splicing	33
Biochemical Insights Into the Conserved Interactions of NMD Factors From Budding Yeast to Humans	33
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	32
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	32
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	32
Direct Actin Monomer Delivery is a WASP-specific Requirement for Arp2/3 Complex Activation	31
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	31
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	30
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	30
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	30
Chaperone Recycling in Late-Stage Flagellar Assembly	30
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	30
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	30
Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos	30
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	30
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	30
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	29
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	29
Structure of the Borrelia Bacteriophage φBB1 Procapsid	29
The Structure of the Full Catalytic Cycle of Vibrio cholerae NFeoB	28
Editorial Board	28
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	28
GRAMMCell: Docking-based Cell Modeling Resource	28
The Role of LRRK2 in Intracellular Organelle Dynamics	28
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	28
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	28
TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway	28
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	27
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	27
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	27
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	27
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	27
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	27
Rising Star: A Unified Mechanism of Plant NLR Immune Signaling	27
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
The Evolution of Sequence Specificity in a DNA Binding Protein Family	26
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	26
memerna: Sparse RNA folding including coaxial stacking	26
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	26
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	25
Rising Stars: Molecular and Functional Diversity of the Sensory Nervous System	25
Editorial Board	25
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	25
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	25
Motif server: web server for undesignable RNA motifs and structures	25
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	25
Structural Analysis of Mammalian Sialic Acid Esterase	24
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	24
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	24
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	24
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	24
Editorial Board	24
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	24
Anthrax Toxin: Model System for Studying Protein Translocation	24
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	24
High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks	24
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	24
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	24
Editorial Board	23
Editorial Board	23
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	23
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	23
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	23
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	23
Editorial Board	23
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	23
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	23
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	23
Outside Front Cover	23
Editorial Board	23
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	23
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	23
Unveiling the UFMylation Pathway: Implications in Neurodegenerative Diseases	22
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	22
Editorial Board	22
Gene2Phenotype: A Database of Structured Human Monogenic Diseases and Pathomechanisms	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
Biophysical Characterization of Recurrent ErbB2 Missense Mutations Reveals Alterations in Receptor Organization and Membrane Dynamics	22

GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	22
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	21
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	21
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	21
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	21
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	21
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	21
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	21
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	21
DeepMS: super-fast peptide identification using end-to-end deep learning method	21
Gene Expression Imaging in Hematopoiesis	20
Editorial Board	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	20
Editorial Board	20
Editorial Board	20
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	20
Global Analysis of Multi-Mutants to Improve Protein Function	20
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	20
Outside Front Cover	20
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	20
Rising Star: Exploring Weak Biomolecular Interactions: My Steady and Evolving Journey	20
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	19
K-Pro: Kinetics Data on Proteins and Mutants	19
Sequence Engineering at Non-motif Modulator Residues Yields a Peptide That Effectively Targets a Single PDZ Protein in a Disease-relevant Cellular Context	19
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	19
Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils	19
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
Rising Star: Rewriting the Code of Life for the Future of Food	19
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	19
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	19
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	19
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	19
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	18
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	18
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	18
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	18
Unexpected Richness of the Bacterial Small RNA World	18
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	18
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	18
PANDA: PAN Cancer Data Analysis Web Tool	18
Selenocysteine-dependent Enzymes: Structure, Function and Selenium-derived Mechanism	18
Formation Mechanism and Antibacterial Activity of Natural Antimicrobial Lysozyme with Antibiotics Doxycycline and Tigecycline	18
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	18
Evolution of Temperature Dependence of TRPM2 Channel Gating and Inactivation in Vertebrates	18
Editorial Board	18
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	18
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	17
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	17
Outside Front Cover	17
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	17
Outside Front Cover	17
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	17
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	17
Outside Front Cover	17
Editorial Board	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	17
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	16
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	16
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	16
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	16
CovInter 2.0: Comprehensive Molecular Interactome of Coronavirus Infection	16
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]	16
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	16
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	16
The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects	16
Signal Propagation Within the MCL-1/BIM Protein Complex	16
The Structure and Function of the Bacterial Osmotically Inducible Protein Y	16
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	16
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	16
From embryos to condensates: A developmental biologist’s journey	15
CEP290 is Associated With Chromatin Accessibility of Hepatitis B virus cccDNA	15
Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs	15
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	15
In Silico Approaches for Prediction of Anti-CRISPR Proteins	15
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	15
Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain	15
CLISGen: A Comprehensive Resource of SNP Genotypes for Human Cell Lines	15
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	15
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	15
Liquid-liquid Phase Separation in Viral Function	14
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription	14
Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future	14
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	14
Channel Gating in Kalium Channelrhodopsin Slow Mutants	14
Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects	14
An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA	14
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	14
Structural Dynamics of Rho GTPases	14
Imaging the Cytoplasmic Lives of Single mRNAs	14
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	14
The Protein Scaffolding Functions of Polyphosphate	14
Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme	14