Journal of Molecular Biology

Article	Citations
Editorial Board	380
Outside Front Cover	147
Outside Front Cover	146
Outside Front Cover	135
Outside Front Cover	122
Outside Front Cover	104
Kinetic Investigation of Resistance to Islatravir Conferred by Mutations in HIV-1 Reverse Transcriptase	96
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	96
Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent	91
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	90
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	86
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	83
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	81
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	81
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	80
Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored	72
Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes	68
Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae	67
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	64
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	63
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	63
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	61
Biomolecular Condensates as Novel Antiviral Targets	60
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	60
HIV-Induced CPSF6 Condensates	57

The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	57
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	55
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	55
Editorial Board	52
The Structure of a Thermostable Phage’s Portal Vertex and Neck Complex Illuminates the Headful Maturation Mechanism	52
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	52
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	51
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	49
ABSEIL: A polypeptide helicity and ensemble prediction tool	49
Cell Lines CoCoPUTs: A Database of Codon and Codon-pair Usage Frequencies in Cell Lines	48
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	48
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	45
ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events	45
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	45
Structural and Functional Characterization of Pseudomonas aeruginosa Virulence Factor AaaA, an Autotransporter with Arginine-Specific Aminopeptidase Activity	44
Mechanisms of Translation-coupled Quality Control	44
Deeptosis: A Deep Learning-Based Platform for Label-Free Discrimination of Apoptosis and Pyroptosis from Brightfield Microscopy	44
Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2	42
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	42
Extracellular uncoating of bacteriophage MS2	41
Pioneers: Glucose Sensing and Control of Health-span and Lifespan	41
Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae	41
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	41
Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms	40
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	40
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation	38
Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis	38
BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele	38
The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study	37
The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery	37
Near-Infrared Optogenetic Module for Conditional Protein Splicing	37
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation	37
AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome	37
Outside Front Cover	36
Editorial Board	36
CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature	36
Editorial Board	36
Outside Front Cover	36
Outside Front Cover	36
Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates	35
GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention	35
Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand	35
Direct Actin Monomer Delivery is a WASP-specific Requirement for Arp2/3 Complex Activation	34
Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis	34
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches	34
The Peripherally Membrane-attached Protein MbFACL6 of Mycobacterium tuberculosis Activates a Broad Spectrum of Substrates	34
Rising Star: G Protein-coupled Receptors (GPCRs) in Microenvironment Pharmacology and Sensory Perception Pharmacology	33
Biochemical Insights Into the Conserved Interactions of NMD Factors From Budding Yeast to Humans	33
Evolution of Transcription Factor-containing Superfamilies in Eukaryotes	33
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures	33

Outside Front Cover	33
GMMA Can Stabilize Proteins Across Different Functional Constraints	33
Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness	32
EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning	32
lncRNAlyzr: Enrichment Analysis for lncRNA Sets	31
Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps	31
Chaperone Recycling in Late-Stage Flagellar Assembly	31
RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces	31
C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies	31
Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution	30
AFflecto: A web server to generate conformational ensembles of flexible proteins from AlphaFold models	30
Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly	30
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints	30
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data	30
Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance	29
Editorial Board	29
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods	29
Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling	28
Editorial Board	28
Deciphering Long-Range Effects of Mutations: An Integrated Approach Using Elastic Network Models and Protein Structure Networks	28
Phospholipid Transport Across the Bacterial Periplasm Through the Envelope-spanning Bridge YhdP	28
NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression	28
J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70	28
TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway	28
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites	28
Electrostatics Drive the Molecular Chaperone BiP to Preferentially Bind Oligomerized States of a Client Protein	27
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
Pulling Forces Dampen Torsional Fluctuations of Actin Filaments and Reduce Cooperative Cofilin Binding	27
Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish	27
Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway	27
The Evolution of Sequence Specificity in a DNA Binding Protein Family	26
Rising Star: A Unified Mechanism of Plant NLR Immune Signaling	26
Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation	26
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814	26
Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch	26
In vitro Evolution of Uracil Glycosylase Towards DnaKJ and GroEL Binding Evolves Different Misfolded States	26
memerna: Sparse RNA folding including coaxial stacking	26
Structure of the Borrelia Bacteriophage φBB1 Procapsid	26
Anthrax Toxin: Model System for Studying Protein Translocation	25
Protein Intrinsic Disorder and Adaptation to Extreme Environments: Resilience of Chaos	25
Allostery and Missense Mutations as Intermittently Linked Promising Aspects of Modern Computational Drug Discovery	25
Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough	24
The Role of LRRK2 in Intracellular Organelle Dynamics	24
Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation	24
Saccharomyces cerevisiae Xrs2 Binds DNA Through Its FHA Domain	24
Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome	24
Rising Stars: Molecular and Functional Diversity of the Sensory Nervous System	24
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor	24
Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice	24
Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins	24
Motif server: web server for undesignable RNA motifs and structures	24
The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy	24
The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation	23
NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species	23
Editorial Board	23
Investigation of Domain Interaction in the Apolipoprotein E Isoforms by HDX-MS	23
Outside Front Cover	23
Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction	23
The Structure of the Full Catalytic Cycle of Vibrio cholerae NFeoB	23
Editorial Board	23
Editorial Board	23
Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8	23
GRAMMCell: Docking-based Cell Modeling Resource	23
Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates	23
Structural Analysis of Mammalian Sialic Acid Esterase	23
Editorial Board	23
Editorial Board	23
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly	23
High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks	23
Gene Expression Imaging in Hematopoiesis	22
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology	22
Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands	22
Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?	22
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	22
Control of Munc13-1 Activity by Autoinhibitory Interactions Involving the Variable N-terminal Region	22
Global Analysis of Multi-Mutants to Improve Protein Function	22
The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23–144) Fibrils	22
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	22
LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks	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	21
GPCRchimeraDB: A Database of Chimeric G Protein-Coupled Receptors (GPCRs) to Assist Their Design	21
Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures	21
psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors	21
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	21
PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences	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
Structural Insights into Tanc1/2 Autoinhibition and Their Implications for NDD Pathogenesis	21
PAS Dimerization at the Nexus of the Mammalian Circadian Clock	21
Corrigendum to “Conformational Transformation and Selection of Synthetic Prion Strains” [J. Mol. Biol. 413(3) (2011) 527–542]	21
UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations	20
Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution	20
The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation	20
DeepMS: super-fast peptide identification using end-to-end deep learning method	20
Editorial Board	20
YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	20
Editorial Board	20
Outside Front Cover	20
Editorial Board	20
Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality	20
Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA	20
Gene2Phenotype: A Database of Structured Human Monogenic Diseases and Pathomechanisms	20
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
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data	19
SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions	19
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	19
K-Pro: Kinetics Data on Proteins and Mutants	19
The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis	19
Rising Star: Rewriting the Code of Life for the Future of Food	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
Editorial Board	19
Unexpected Richness of the Bacterial Small RNA World	18
Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain	18
Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils	18
Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring	18
PANDA: PAN Cancer Data Analysis Web Tool	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
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust	18
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures	18
MERIT: Accurate Prediction of Multi Ligand-binding Residues with Hybrid Deep Transformer Network, Evolutionary Couplings and Transfer Learning	18
Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis	18
Antibody and B-cell Immune Responses Against Bordetella Pertussis Following Infection and Immunization	18
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	18
AmIActive (AIA): A Large-scale QSAR Based Target Fishing and Polypharmacology Predictive Web Tool	18
An Inner Mitochondrial Membrane Microprotein from the SLC35A4 Upstream ORF Regulates Cellular Metabolism	17
Outside Front Cover	17
Structural Basis of Main Proteases of Coronavirus Bound to Bofutrelvir	17
DciA, the Bacterial Replicative Helicase Loader, Promotes LLPS in the Presence of ssDNA	17
Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules	17
Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function	17
Outside Front Cover	17
A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression	17
Editorial Board	17
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model	17
Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome	17
An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells	17
Outside Front Cover	17
Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC	16
The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects	16
Structural Dynamics of Rho GTPases	16
CovInter 2.0: Comprehensive Molecular Interactome of Coronavirus Infection	16
Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery	16
The Functional Relationship Between RNA Splicing and the Chromatin Landscape	16
Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design	16
Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA	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
Signal Propagation Within the MCL-1/BIM Protein Complex	16
The Structure and Function of the Bacterial Osmotically Inducible Protein Y	16
Liquid-liquid Phase Separation in Viral Function	16
Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?	16
Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction	16
Channel Gating in Kalium Channelrhodopsin Slow Mutants	15
Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication	15
PerturbSeq.db: An Integrated Repository for Comprehensive Analysis of Single-cell Perturbation Data	15
Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins	15
Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities	15
Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir	15
SSP: An In Silico Tool for Salmonella Species Serotyping Using the Sequences of O-Antigen Biosynthesis Proteins and H-Antigen Filament Proteins	15
An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA	14
Isotopologues of a Metabolic Precursor for Selective N-15 and C-13 Histidine Labeling	14
Sequence Determinants of Allosteric Back-to-front Control of the Arf Nucleotide Switch	14
Editorial Board	14
The Protein Scaffolding Functions of Polyphosphate	14
Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain	14
Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme	14
Imaging the Cytoplasmic Lives of Single mRNAs	14
Editorial Board	14
A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread	14
Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication	14
Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin	14
mdxplain: Scalable molecular dynamics analysis with machine learning-based feature selection and modular workflows	14
Loss of Residues 119–136, Including the First β-strand of Human Prion Protein, Generates an Aggregation-competent Partially “Open” Form	14