Journal of Molecular Biology

Article	Citations
Editorial Board	433
Outside Front Cover	263
Outside Front Cover	165
Outside Front Cover	128
Outside Front Cover	123
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	112
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	108
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	98
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	88
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	88
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	86
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	80
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	78
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	73
Editorial Board	70
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	70
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	70
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	64
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	63
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	59
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	59
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	57
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	57
19F NMR Strategy for Probing Site-specific RNA Dynamics in Large RNA-protein Complexes: Application to the Hfq RNA Chaperone	55
Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae	54

NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	52
Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae	52
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	52
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	51
Biomolecular Condensates as Novel Antiviral Targets	49
Mechanisms of Translation-coupled Quality Control	48
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	48
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	48
Extracellular uncoating of bacteriophage MS2	46
Pioneers: Glucose Sensing and Control of Health-span and Lifespan	45
The Structure of a Thermostable Phage’s Portal Vertex and Neck Complex Illuminates the Headful Maturation Mechanism	45
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	44
HIV-Induced CPSF6 Condensates	43
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	43
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	43
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	43
Editorial Board	42
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	42
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	42
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	42
Editorial Board	41
Outside Front Cover	41
Outside Front Cover	41
Outside Front Cover	40
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	39
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	39
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	38
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	38
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	38
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	38
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	38
Near-Infrared Optogenetic Module for Conditional Protein Splicing	37
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	37
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	36
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	36
Direct Actin Monomer Delivery is a WASP-specific Requirement for Arp2/3 Complex Activation	36
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	35
Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis	35
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	35
GMMA Can Stabilize Proteins Across Different Functional Constraints	34
Rising Star: G Protein-coupled Receptors (GPCRs) in Microenvironment Pharmacology and Sensory Perception Pharmacology	34
DIS3L2 and Nonsense-mediated Decay: United to Degrade	34
Chaperone Recycling in Late-Stage Flagellar Assembly	34
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	34
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	34
Outside Front Cover	34
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	33
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	33
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	32
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	32

AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	32
Bacterial Countermeasures Against Inflammasomes	32
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	32
Biochemical Insights Into the Conserved Interactions of NMD Factors From Budding Yeast to Humans	32
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	32
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	32
GRAMMCell: Docking-based Cell Modeling Resource	31
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	31
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	31
The Role of LRRK2 in Intracellular Organelle Dynamics	31
ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis	30
Rising Stars: Molecular and Functional Diversity of the Sensory Nervous System	30
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	30
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	30
The Structure of the Full Catalytic Cycle of Vibrio cholerae NFeoB	30
Editorial Board	30
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	30
Rising Star: A Unified Mechanism of Plant NLR Immune Signaling	30
Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos	30
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	29
The Evolution of Sequence Specificity in a DNA Binding Protein Family	29
Editorial Board	29
memerna: Sparse RNA folding including coaxial stacking	29
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	29
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	28
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	28
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	28
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	28
Obituary for Georg E. Schulz	28
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	28
TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway	27
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	27
Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering	27
High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks	27
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	27
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	26
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	26
Structure of the Borrelia Bacteriophage φBB1 Procapsid	26
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	26
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	26
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	25
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	25
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	25
Editorial Board	25
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	25
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	25
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	25
Outside Front Cover	25
Editorial Board	25
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	25
Anthrax Toxin: Model System for Studying Protein Translocation	25
Editorial Board	25
Editorial Board	25
Editorial Board	25
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	25
Gene Expression Imaging in Hematopoiesis	24
Editorial Board	24
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	24
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	24
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	24
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	24
Global Analysis of Multi-Mutants to Improve Protein Function	24
Unveiling the UFMylation Pathway: Implications in Neurodegenerative Diseases	24
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	23
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	23
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	23
DeepMS: super-fast peptide identification using end-to-end deep learning method	23
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	23
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	23
Structural Analysis of Mammalian Sialic Acid Esterase	22
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Biophysical Characterization of Recurrent ErbB2 Missense Mutations Reveals Alterations in Receptor Organization and Membrane Dynamics	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	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
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	22
Structural Insights into Tanc1/2 Autoinhibition and Their Implications for NDD Pathogenesis	22
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	22

Editorial Board	21
Editorial Board	21
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	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
Editorial Board	21
Selenocysteine-dependent Enzymes: Structure, Function and Selenium-derived Mechanism	21
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	21
Outside Front Cover	21
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	21
Formation Mechanism and Antibacterial Activity of Natural Antimicrobial Lysozyme with Antibiotics Doxycycline and Tigecycline	21
PANDA: PAN Cancer Data Analysis Web Tool	20
Editorial Board	20
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	20
TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data	20
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	20
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	20
K-Pro: Kinetics Data on Proteins and Mutants	20
Rising Star: Rewriting the Code of Life for the Future of Food	19
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	19
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	19
Evolution of Temperature Dependence of TRPM2 Channel Gating and Inactivation in Vertebrates	19
Rising Star: Exploring Weak Biomolecular Interactions: My Steady and Evolving Journey	19
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	19
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	19
Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils	19
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	19
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	19
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	19
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	19
Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging	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
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	18
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	18
Outside Front Cover	18
Outside Front Cover	18
Unexpected Richness of the Bacterial Small RNA World	18
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	18
Surveying bacterial microcompartment core enzymes to identify prospective encapsulation peptides and principles of core interactions	18
Editorial Board	18
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	18
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	18
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	18
Outside Front Cover	18
Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain	17
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	17
The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition	17
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	17
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	17
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	17
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	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
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	17
From embryos to condensates: A developmental biologist’s journey	17
Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs	17
Mitochondrial tRNA-specific Taurine Modifications Correlate With Ferroptosis-associated Myocardial Injury	17
Structural Dynamics of Rho GTPases	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	17
Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch	17
Sequence Determinants of Allosteric Back-to-front Control of the Arf Nucleotide Switch	16
Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme	16
An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA	16
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	16
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	16
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	16
Imaging the Cytoplasmic Lives of Single mRNAs	16
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	16
The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects	16
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	16
The Structure and Function of the Bacterial Osmotically Inducible Protein Y	16
Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future	16
Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR	16
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	16
Outside Front Cover	16
Channel Gating in Kalium Channelrhodopsin Slow Mutants	16
CEP290 is Associated With Chromatin Accessibility of Hepatitis B virus cccDNA	16
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	16
Editorial Board	15
In Silico Approaches for Prediction of Anti-CRISPR Proteins	15
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	15
The Functional Relationship Between RNA Splicing and the Chromatin Landscape	15
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	15
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription	15
Outside Front Cover	15
Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design	15
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	15
Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects	15
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	15
Editorial Board	15
Outside Front Cover	15
Liquid-liquid Phase Separation in Viral Function	15
Signal Propagation Within the MCL-1/BIM Protein Complex	15
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	15
The Protein Scaffolding Functions of Polyphosphate	15