Journal of Molecular Biology

Article	Citations
Editorial Board	435
Editorial Board	319
The RNA-Binding Properties of Annexins	234
ProtSpace: A Tool for Visualizing Protein Space	201
Outside Front Cover	184
Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8	184
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	181
Recognition Mechanism of RNA by TLR13: Structural Insights and Implications for Immune Activation	161
Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter	135
Editorial Board	118
Disordered Regions of Condensate-promoting Proteins Have Distinct Molecular Signatures Associated with Cellular Function	107
Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses	107
Advances in Protein Structure Prediction Highlight Unexpected Commonalities Between Gram-positive and Gram-negative Conjugative T4SSs	102
The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations	101
Editorial Board	93
Structural Basis for C2′-methoxy Recognition by DNA Polymerases and Function Improvement	90
The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication Primarily Via Cluster Member miR-92a	88
Phyre2.2: A Community Resource for Template-based Protein Structure Prediction	84
@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking	84
Editorial Board	84
Effectiveness and Efficiency: Label-Aware Hierarchical Subgraph Learning for Protein–Protein Interaction	78
The Prediction of Recombination Hotspot Based on Automated Machine Learning	78
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	77
TCM-ADIP: A Multidimensional Database Linking Traditional Chinese Medicine to Functional Brain Zones of Alzheimer’s Disease	76
Emerging Artificial Intelligence Methodologies in Computational Biology	76

Outside Front Cover	75
Predicting Metal-binding Proteins and Structures Through Integration of Evolutionary-scale and Physics-based Modeling	75
Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models	74
Outside Front Cover	73
The Carbonyl Group in β2 of the Carotenoid Tunes the Photocycle Kinetics in Orange Carotenoid Protein	72
Structural Basis of DEPTOR to Recognize Phosphatidic Acid Using its Tandem DEP Domains	72
Molecular mechanisms and functions of pyroptosis	71
Structure and the Mode of Activity of Lon Proteases from Diverse Organisms	71
Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo	71
Editorial Board	69
Outside Front Cover	69
Outside Front Cover	67
Editorial Board	66
Protein-Membrane Interaction at the Pre-Synapse	65
Minireview: What is Known about SUMOylation Among NR4A Family Members?	63
Outside Front Cover	61
Outside Front Cover	61
Mechanical Stress Decreases the Amplitude of Twisting and Bending Fluctuations of Actin Filaments	60
Outside Front Cover	60
Editorial Board	60
Editorial Board	59
Paths Through the Yeast Regulatory Network in Different Physiological States	58
Outside Front Cover	57
Editorial Board	55
Outside Front Cover	55
Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human α2δ1, a Voltage-Gated Calcium Channel Subunit	54
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	54
Outside Front Cover	53
Outside Front Cover	52
Outside Front Cover	52
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	52
Recent Advances in Genetic Code Expansion: From Cell Engineering to Protein Design	51
Editorial Board	50
Molecular Mechanisms and Physiological Functions of Autophagy	50
Editorial Board	49
Editorial Board	49
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	48
Editorial Board	48
Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor	47
The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development	47
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	46
Outside Front Cover	46
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins	45
Cholesterol-Mediated Clustering of the HIV Fusion Protein gp41 in Lipid Bilayers	45
Outside Front Cover	43
EvoRator: Prediction of Residue-level Evolutionary Rates from Protein Structures Using Machine Learning	43
Two Bacterial Small Heat Shock Proteins, IbpA and IbpB, Form a Functional Heterodimer	43
Editorial Board	43
Structural Insights into the Catalytic Cycle of a Bacterial Multidrug ABC Efflux Pump	42
RNASequest: An End-to-End Reproducible RNAseq Data Analysis and Publishing Framework	42

The Extraction Mechanism of Monoubiquitinated PEX5 from the Peroxisomal Membrane	42
Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane	41
Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10	40
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	40
The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1)	39
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	39
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	39
Therapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families	39
Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria	39
Subsets of Slow Dynamic Modes Reveal Global Information Sources as Allosteric Sites	39
Identification and Characterization of the Interaction Between the Methyl-7-Guanosine Cap Maturation Enzyme RNMT and the Cap-Binding Protein eIF4E	38
GCN2 in Viral Defence and the Subversive Tactics Employed by Viruses	38
Protein interactions in liquid–liquid phase separation	38
Single Amino Acid Mutation Decouples Photochemistry of the BLUF Domain from the Enzymatic Function of OaPAC and Drives the Enzyme to a Switched-on State	37
High Risk, High Reward: By Selecting Tsg101, A Protein That Sorts The Trash, As Our Personal ESCRT, Both HIV And I Were Able To Bud	36
Ion Channels: Intersection of Structure, Function, and Pharmacology	36
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	36
Mono- and Bi-specific Nanobodies Targeting the CUB Domains of PCPE-1 Reduce the Proteolytic Processing of Fibrillar Procollagens	36
Morpholinium-based Ionic Liquids as Potent Antibiofilm and Sensitizing Agents for the Control of Pseudomonas aeruginosa	35
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	35
MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation	35
The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways	35
BCG-Induced Immune Training: Interplay between Trained Immunity and Emergency Granulopoiesis	34
Nucleosome Positioning on Large Tandem DNA Repeats of the ‘601’ Sequence Engineered in Saccharomyces cerevisiae	34
Editorial Board	34
AIDA-1/ANKS1B Binds to the SynGAP Family RasGAPs with High Affinity and Specificity	34
Outside Front Cover	33
Phospholipid Supply for Autophagosome Biogenesis	32
ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities	32
Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention	32
Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures	32
Real-time Exchange of the Lipid-bound Intermediate and Post-fusion States of the HIV-1 gp41 Ectodomain	32
BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins	32
Structural and Dynamic Changes of Nucleosome upon GATA3 Binding	31
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	31
Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease	30
PhosphoFlowSeq – A High-throughput Kinase Activity Assay for Screening Drug Resistance Mutations in EGFR	30
Biochemical Timekeeping Via Reentrant Phase Transitions	30
The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex	30
CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Koh	30
Subunit Communication within Dimeric SF1 DNA Helicases	30
MVAR: A Mouse Variation Registry	29
Mutual Protein-Ligand Conformational Selection Drives cGMP vs. cAMP Selectivity in Protein Kinase G	29
Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution	29
Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4	29
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	28
Structure of the Anthrax Protective Antigen D425A Dominant Negative Mutant Reveals a Stalled Intermediate State of Pore Maturation	28
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	28
A Novel Mechanism of Coactivator Recruitment by the Nurr1 Nuclear Receptor	27
Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation	27
Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form	27
Structure of Essential RNA Regulatory Elements in the West Nile Virus 3′-Terminal Stem Loop	27
Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models	26
Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression	26
GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network	26
Biochemical Characterization of Cell-free Synthesized Human β1 Adrenergic Receptor Cotranslationally Inserted into Nanodiscs	26
Potential vs Challenges of Expanding the Protein Universe With Genetic Code Expansion in Eukaryotic Cells	26
Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins	26
Selective Inhibition of Cysteine-Dependent Enzymes by Bioorthogonal Tethering	26
Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research	26
The Structural Stability of Membrane Proteins Revisited: Combined Thermodynamic and Spectral Phasor Analysis of SDS-induced Denaturation of a Thermophilic Cu(I)-transport ATPase	25
Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data	25
Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance	24
Modification of Regulatory Tyrosine Residues Biases Human Hsp90α in its Interactions with Cochaperones and Clients	24
Structural Basis of the Selective Sugar Transport in Sodium-Glucose Cotransporters	24
Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis	24
N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins	24
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	24
Simplicity is the Ultimate Sophistication—Crosstalk of Post-translational Modifications on the RNA Polymerase II	24
The Core Complex of the Ca2+-Triggered Presynaptic Fusion Machinery	23
Eukaryotic Initiation Factor 5A2 Regulates Expression of Antiviral Genes	23
Can We AlphaFold Our Way Out of the Next Pandemic?	23
Ca2+ and Mg2+ Influence the Thermodynamics of Peptide-Membrane Interactions	23
MRT-ModSeq – Rapid Detection of RNA Modifications with MarathonRT	23
Conserved and Unique Roles of bHLH-PAS Transcription Factors in Insects – From Clock to Hormone Reception	23
Enhancer Dependent Repositioning of TCRb Locus with Respect to the Chromosome Territory	23
Dynamics of the Artemis and DNA-PKcs Complex in the Repair of Double-Strand Breaks	23
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	23
Conservation and Diversity in Allosteric Fingerprints of Proteins for Evolutionary-inspired Engineering and Design	23
Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons	23

Deep Learning to Predict the Biosynthetic Gene Clusters in Bacterial Genomes	23
Yeast Proteins may Reversibly Aggregate like Amphiphilic Molecules	23
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	23
Intein-based Design Expands Diversity of Selenocysteine Reporters	23
HDX-MS and MD Simulations Provide Evidence for Stabilization of the IgG1—FcγRIa (CD64a) Immune Complex Through Intermolecular Glycoprotein Bonds	23
C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database	23
The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme	23
A Novel, Universally Active C-terminal Protein Degradation Signal Generated by Alternative Splicing	23
Probing the Interaction Between Supercarrier RBC Membrane and Nanoparticles for Optimal Drug Delivery	23
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	23
Why Does Synergistic Activation of WASP, but Not N-WASP, by Cdc42 and PIP2 Require Cdc42 Prenylation?	23
D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences	22
Cellular Assays for Dynamic Quantification of Deubiquitinase Activity and Inhibition	22
Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A?	22
Isling: A Tool for Detecting Integration of Wild-Type Viruses and Clinical Vectors	22
The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains	22
Role of Ion Distribution and Energy Barriers for Concerted Motion of Subunits in Selectivity Filter Gating of a K+ Channel	22
A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine	22
Solution Structure of Poly(UG) RNA	22
CM2D3: Furnishing the Human Interactome with Structural Models of Protein Complexes Derived by Comparative Modeling and Docking	22
A Novel Approach for the Synthesis of Human Heteropolymer Ferritins of Different H to L Subunit Ratios	22
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile	22
PDGF-D Prodomain Differentially Inhibits the Biological Activities of PDGF-D and PDGF-B	22
Interactions between Ligand-Bound EGFR and VEGFR2	22
Cross-over Loop Cysteine C152 Acts as an Antioxidant to Maintain the Folding Stability and Deubiquitinase Activity of UCH-L1 Under Oxidative Stress	22
Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates	22
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	22
Genetic Code Expansion Through Quadruplet Codon Decoding	21
Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei	21
Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms	21
FIP200 Phosphorylation Regulates Late Steps in Mitophagy	21
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	21
Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase	21
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	21
Mechanisms of Gasdermin Recognition by Proteases	21
Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps	21
Special Issue: Proteostasis and Protein Quality Control	21
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements	21
Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA	20
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	20
Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome	20
Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors	20
PrimPol Variant V102A with Altered Primase and Polymerase Activities	20
Inventing Novel Protein Folds	20
An Atypical Mechanism of SUMOylation of Neurofibromin SecPH Domain Provides New Insights into SUMOylation Site Selection	20
CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation	20
Mechanistic Basis for a Single Amino Acid Residue Mutation Causing Human DNA Ligase 1 Deficiency, A Rare Pediatric Disease	20
Cholesterol Binds the Amphipathic Helix of IFITM3 and Regulates Antiviral Activity	20
Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold	19
Identification of a Catalytic Lysine Residue Conserved Among GHKL ATPases: MutL, GyrB, and MORC	19
Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins	19
Biomolecular Condensates as Novel Antiviral Targets	19
Two Closed Conformations of CRAF Require the 14-3-3 Binding Motifs and Cysteine-Rich Domain to be Intact in Live Cells	19
The Viral Protein K7 Inhibits Biochemical Activities and Condensate Formation by the DEAD-box Helicase DDX3X	19
Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix Metalloproteinase Inhibitor	19
Corrigendum to “The C-terminal Domain of piggyBac Transposase is not Required for DNA Transposition” [J. Mol. Biol. 433 (2021) 166805]	19
Identification of a Non-canonical Function of Prefoldin Subunit 5 in Proteasome Assembly	19
Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery	19
The Hydrophilic C-terminus of Yeast Plasma-membrane Na+/H+ Antiporters Impacts Their Ability to Transport K+	19
Transcriptional and Epigenetic Regulation of Gasdermins	19
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	19
Corrigendum to “PARP Activity Fine-tunes the DNA Replication Choreography of Chk1-depleted Cells” [J. Mol. Biol. 433(10) (2021) 166949]	18
Designer Condensates: A Toolkit for the Biomolecular Architect	18
IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data	18
Spn1 and Its Dynamic Interactions with Spt6, Histones and Nucleosomes	18
Facile Method for High-throughput Identification of Stabilizing Mutations	18
Understanding the role of tRNA modifications in UGA recoding as selenocysteine in eukaryotes	18
Pyroptosis in Steatohepatitis and Liver Diseases	18
5-Methyluridine is Ubiquitous in Pseudomonas aeruginosa tRNA and Modulates Antimicrobial Resistance and Virulence	18
The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives	18
Mechanisms of Translation-coupled Quality Control	18
Editorial Board	18
Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation	18
The Folding Pathway of ABC Transporter CFTR: Effective and Robust	18
Enzymatic Reactions inside Biological Condensates	18
From Rat Tails to Glycoproteostasis: Motivated by Biology, Enabled by Biophysics, and Lucky	18
Protein Misfolding Releases Human HSF1 from HSP70 Latency Control	17
Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins	17
Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-κB 1 (ABIN1) and M1-Linked Ubiquitins	17
Terminase Subunits from the Pseudomonas-Phage E217	17
Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM	17
MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences	17
KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions	17
Troponin Structural Dynamics in the Native Cardiac Thin Filament Revealed by Cryo Electron Microscopy	17
Dityrosine Cross-links are Present in Alzheimer’s Disease-derived Tau Oligomers and Paired Helical Filaments (PHF) which Promotes the Stability of the PHF-core Tau (297–391) In Vitro	17
HTSDSF Explorer, A Novel Tool to Analyze High-throughput DSF Screenings	17
CavityPlus 2022 Update: An Integrated Platform for Comprehensive Protein Cavity Detection and Property Analyses with User-friendly Tools and Cavity Databases	17
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive	17
Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils	17
DNA Vaccines: History, Molecular Mechanisms and Future Perspectives	17
Intrinsic Disorder in Human RNA-Binding Proteins	17
Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin’s A-B Subunit Interface	17
Kinetic investigation of resistance to Islatravir conferred by mutations in HIV-1 reverse transcriptase	17
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation	17
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	17