Journal of Molecular Biology

Article	Citations
Editorial Board	391
Editorial Board	279
Phyre2.2: A community resource for template-based protein structure prediction	191
Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold	184
GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network	182
Identification of a Non-canonical Function of Prefoldin Subunit 5 in Proteasome Assembly	171
The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex	144
The Role of ATG9 Vesicles in Autophagosome Biogenesis	141
PrimPol Variant V102A with Altered Primase and Polymerase Activities	118
CM2D3: Furnishing the Human Interactome with Structural Models of Protein Complexes Derived by Comparative Modeling and Docking	101
Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease	94
RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs	88
MVAR: A Mouse Variation Registry	87
Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins	87
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures	85
Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research	84
CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation	78
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins	74
Structural Basis for C2′-methoxy Recognition by DNA Polymerases and Function Improvement	73
Editorial Board	73
Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases	72
Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery	70
The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication Primarily Via Cluster Member miR-92a	70
PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning	68
Spn1 and Its Dynamic Interactions with Spt6, Histones and Nucleosomes	67

Mechanisms of Gasdermin Recognition by Proteases	66
@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking	65
Nucleation-dependent Aggregation Kinetics of Yeast Sup35 Fragment GNNQQNY	65
Outside Front Cover	64
Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel	61
Effectiveness and Efficiency: Label-Aware Hierarchical Subgraph Learning for Protein–Protein Interaction	61
Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form	61
The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis	61
Intrinsic Disorder of the Neuronal SNARE Protein SNAP25a in its Pre-fusion Conformation	60
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region	60
Selective Inhibition of Cysteine-Dependent Enzymes by Bioorthogonal Tethering	58
A Novel, Universally Active C-terminal Protein Degradation Signal Generated by Alternative Splicing	57
Outside Front Cover	57
Editorial Board	56
Outside Front Cover	55
Editorial Board	54
Respiratory Syncytial Virus NS1 Protein Targets the Transactivator Binding Domain of MED25	53
MRT-ModSeq – Rapid Detection of RNA Modifications with MarathonRT	52
FDX1 Is Required for the Biogenesis of Mitochondrial Cytochrome c Oxidase in Mammalian Cells	52
D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences	52
Protein-Membrane Interaction at the Pre-Synapse	50
Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei	49
Outside Front Cover	48
Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-κB 1 (ABIN1) and M1-Linked Ubiquitins	47
Outside Front Cover	47
Editorial Board	47
Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis	46
Ca2+ and Mg2+ Influence the Thermodynamics of Peptide-Membrane Interactions	46
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification	46
Mechanical Stress Decreases the Amplitude of Twisting and Bending Fluctuations of Actin Filaments	45
Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A?	45
Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins	45
Outside Front Cover	45
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)	44
Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates	43
Editorial Board	43
Outside Front Cover	43
Paths Through the Yeast Regulatory Network in Different Physiological States	43
Outside Front Cover	42
Editorial Board	42
High-resolution Crystal Structure of Human pERp1, A Saposin-like Protein Involved in IgA, IgM and Integrin Maturation in the Endoplasmic Reticulum	41
Quantitation of Human 14-3-3ζ Dimerization and the Effect of Phosphorylation	41
Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope	40
An Alternative Role of RluD in the Fidelity of Translation Initiation in Escherichia coli	40
Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution	40
Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome	39
Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human α2δ1, a Voltage-Gated Calcium Channel Subunit	39
Terminase Subunits from the Pseudomonas-Phage E217	39
Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6	38
Biochemical Characterization of Cell-free Synthesized Human β1 Adrenergic Receptor Cotranslationally Inserted into Nanodiscs	38

Enhancer Dependent Repositioning of TCRb Locus with Respect to the Chromosome Territory	37
Eukaryotic Initiation Factor 5A2 Regulates Expression of Antiviral Genes	36
Structure of the Anthrax Protective Antigen D425A Dominant Negative Mutant Reveals a Stalled Intermediate State of Pore Maturation	36
Outside Front Cover	35
Mechanisms of PAS Domain Signalling, from Sensing Varied Small Molecules and Peptides to Approved Pharmaceuticals and Use in Optogenetics	35
Outside Front Cover	35
PDGF-D Prodomain Differentially Inhibits the Biological Activities of PDGF-D and PDGF-B	35
Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase	34
Molecular Mechanisms and Physiological Functions of Autophagy	34
Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance	34
Recent Advances in Genetic Code Expansion: From Cell Engineering to Protein Design	34
Solution Structure of Poly(UG) RNA	33
Editorial Board	33
C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database	33
Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4	32
Editorial Board	32
Inventing Novel Protein Folds	32
Editorial Board	32
Potential vs Challenges of Expanding the Protein Universe With Genetic Code Expansion in Eukaryotic Cells	32
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections	31
Editorial Board	31
Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo	31
Slow Misfolding of a Molten Globule form of a Mutant Prion Protein Variant into a β-rich Dimer	31
The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development	30
Outside Front Cover	30
Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor	30
Can We AlphaFold Our Way Out of the Next Pandemic?	30
The Carbonyl Group in β2 of the Carotenoid Tunes the Photocycle Kinetics in Orange Carotenoid Protein	30
Outside Front Cover	30
Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation	29
Special Issue: Proteostasis and Protein Quality Control	29
Two Closed Conformations of CRAF Require the 14-3-3 Binding Motifs and Cysteine-Rich Domain to be Intact in Live Cells	29
The Folding Pathway of ABC Transporter CFTR: Effective and Robust	29
Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors	28
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements	28
Minireview: What is Known about SUMOylation Among NR4A Family Members?	28
Inhibition of SARS-CoV-2 Infection by Human Defensin HNP1 and Retrocyclin RC-101	27
Outside Front Cover	27
IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy	27
Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter	27
Probing the Interaction Between Supercarrier RBC Membrane and Nanoparticles for Optimal Drug Delivery	26
The Extraction Mechanism of Monoubiquitinated PEX5 from the Peroxisomal Membrane	26
Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention	26
EvoRator: Prediction of Residue-level Evolutionary Rates from Protein Structures Using Machine Learning	26
Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap	25
Why Does Synergistic Activation of WASP, but Not N-WASP, by Cdc42 and PIP2 Require Cdc42 Prenylation?	25
Facile Method for High-throughput Identification of Stabilizing Mutations	25
Structural Insights into the Catalytic Cycle of a Bacterial Multidrug ABC Efflux Pump	25
Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment	25
RNASequest: An End-to-End Reproducible RNAseq Data Analysis and Publishing Framework	25
A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine	24
MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences	24
A Novel Mechanism of Coactivator Recruitment by the Nurr1 Nuclear Receptor	24
Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State	24
Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane	24
Real-time Exchange of the Lipid-bound Intermediate and Post-fusion States of the HIV-1 gp41 Ectodomain	24
The Viral Protein K7 Inhibits Biochemical Activities and Condensate Formation by the DEAD-box Helicase DDX3X	24
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface	24
Structural Model of the Human BTG2–PABPC1 Complex by Combining Mutagenesis, NMR Chemical Shift Perturbation Data and Molecular Docking	23
Genetic Code Expansion Through Quadruplet Codon Decoding	23
GCN2 in Viral Defence and the Subversive Tactics Employed by Viruses	23
Activation and Evasion of Innate Immunity by Gammaherpesviruses	23
The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains	23
Structure-based Development of Human Interleukin-1β-Specific Antibody That Simultaneously Inhibits Binding to Both IL-1RI and IL-1RAcP	23
Dissecting the Binding Interface of the Septin Polymerization Enhancer Borg BD3	23
Protein interactions in liquid–liquid phase separation	23
Identification and Characterization of the Interaction Between the Methyl-7-Guanosine Cap Maturation Enzyme RNMT and the Cap-Binding Protein eIF4E	23
Interactions between Ligand-Bound EGFR and VEGFR2	23
Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure	23
Cross-over Loop Cysteine C152 Acts as an Antioxidant to Maintain the Folding Stability and Deubiquitinase Activity of UCH-L1 Under Oxidative Stress	22
Ion Channels: Intersection of Structure, Function, and Pharmacology	22
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	22
HTSDSF Explorer, A Novel Tool to Analyze High-throughput DSF Screenings	22
FIP200 Phosphorylation Regulates Late Steps in Mitophagy	22
Identification of a Catalytic Lysine Residue Conserved Among GHKL ATPases: MutL, GyrB, and MORC	22
Two Bacterial Small Heat Shock Proteins, IbpA and IbpB, Form a Functional Heterodimer	22
The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways	22
The Disordered MAX N-terminus Modulates DNA Binding of the Transcription Factor MYC:MAX	22
Recent Advances in Genetic Code Expansion Techniques for Protein Phosphorylation Studies	22
Molecular mechanisms and functions of pyroptosis	22

Competitive Microtubule Binding of PEX14 Coordinates Peroxisomal Protein Import and Motility	22
HIV-Induced CPSF6 Condensates	21
Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons	21
Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data	21
MuA-based Molecular Indexing for Rare Mutation Detection by Next-Generation Sequencing	21
Structure and the Mode of Activity of Lon Proteases from Diverse Organisms	20
N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins	20
MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation	20
Nucleosome Positioning on Large Tandem DNA Repeats of the ‘601’ Sequence Engineered in Saccharomyces cerevisiae	20
Yeast Proteins may Reversibly Aggregate like Amphiphilic Molecules	20
Intein-based Design Expands Diversity of Selenocysteine Reporters	20
The Hydrophilic C-terminus of Yeast Plasma-membrane Na+/H+ Antiporters Impacts Their Ability to Transport K+	20
Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae	20
Morpholinium-based Ionic Liquids as Potent Antibiofilm and Sensitizing Agents for the Control of Pseudomonas aeruginosa	20
Role of Ion Distribution and Energy Barriers for Concerted Motion of Subunits in Selectivity Filter Gating of a K+ Channel	20
Molecular Mechanism of Nramp-Family Transition Metal Transport	20
ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities	19
Structural and Dynamic Changes of Nucleosome upon GATA3 Binding	19
Dynamic Processing of a Common Oxidative DNA Lesion by the First Two Enzymes of the Base Excision Repair Pathway	19
Dynamics of the Artemis and DNA-PKcs Complex in the Repair of Double-Strand Breaks	19
Deep Learning to Predict the Biosynthetic Gene Clusters in Bacterial Genomes	19
Designer Condensates: A Toolkit for the Biomolecular Architect	19
BCG-Induced Immune Training: Interplay between Trained Immunity and Emergency Granulopoiesis	19
Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin’s A-B Subunit Interface	19
The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme	19
Structures of Native-like Nucleosomes: One Step Closer toward Understanding the Structure and Function of Chromatin	19
Cholesterol Binds the Amphipathic Helix of IFITM3 and Regulates Antiviral Activity	19
Isling: A Tool for Detecting Integration of Wild-Type Viruses and Clinical Vectors	19
Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle	18
The Structural Stability of Membrane Proteins Revisited: Combined Thermodynamic and Spectral Phasor Analysis of SDS-induced Denaturation of a Thermophilic Cu(I)-transport ATPase	18
An Atypical Mechanism of SUMOylation of Neurofibromin SecPH Domain Provides New Insights into SUMOylation Site Selection	18
Engineered mRNAs With Stable Structures Minimize Double-stranded RNA Formation and Increase Protein Expression	18
AIDA-1/ANKS1B Binds to the SynGAP Family RasGAPs with High Affinity and Specificity	18
Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms	18
Mono- and Bi-specific Nanobodies Targeting the CUB Domains of PCPE-1 Reduce the Proteolytic Processing of Fibrillar Procollagens	18
Structure of Essential RNA Regulatory Elements in the West Nile Virus 3′-Terminal Stem Loop	18
Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA	18
KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions	18
Mechanistic Basis for a Single Amino Acid Residue Mutation Causing Human DNA Ligase 1 Deficiency, A Rare Pediatric Disease	18
Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models	18
Modification of Regulatory Tyrosine Residues Biases Human Hsp90α in its Interactions with Cochaperones and Clients	18
Conserved and Unique Roles of bHLH-PAS Transcription Factors in Insects – From Clock to Hormone Reception	18
Editorial Board	18
Cellular Assays for Dynamic Quantification of Deubiquitinase Activity and Inhibition	17
HDX-MS and MD Simulations Provide Evidence for Stabilization of the IgG1—FcγRIa (CD64a) Immune Complex Through Intermolecular Glycoprotein Bonds	17
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation	17
Protein Misfolding Releases Human HSF1 from HSP70 Latency Control	17
Phospholipid Supply for Autophagosome Biogenesis	17
Subsets of Slow Dynamic Modes Reveal Global Information Sources as Allosteric Sites	17
The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1)	17
How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein	17
Free Energy Landscape of H2A-H2B Displacement From Nucleosome	17
Outside Front Cover	17
Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8	17
Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins	17
CavityPlus 2022 Update: An Integrated Platform for Comprehensive Protein Cavity Detection and Property Analyses with User-friendly Tools and Cavity Databases	17
Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria	17
Therapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families	17
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain	17
Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture	17
Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures	16
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes	16
Simplicity is the Ultimate Sophistication—Crosstalk of Post-translational Modifications on the RNA Polymerase II	16
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	16
Biochemical Timekeeping Via Reentrant Phase Transitions	16
Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils	16
A Novel Approach for the Synthesis of Human Heteropolymer Ferritins of Different H to L Subunit Ratios	16
Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps	16
Pyroptosis in Steatohepatitis and Liver Diseases	16
Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures	16
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	16
The Core Complex of the Ca2+-Triggered Presynaptic Fusion Machinery	16
DNA Vaccines: History, Molecular Mechanisms and Future Perspectives	16
Mutual Protein-Ligand Conformational Selection Drives cGMP vs. cAMP Selectivity in Protein Kinase G	16
Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures	16
Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM	16
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	16
Yorkie-Warts Complexes are an Ensemble of Interconverting Conformers Formed by Multivalent Interactions	16
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive	15
Corrigendum to “The C-terminal Domain of piggyBac Transposase is not Required for DNA Transposition” [J. Mol. Biol. 433 (2021) 166805]	15
PhosphoFlowSeq – A High-throughput Kinase Activity Assay for Screening Drug Resistance Mutations in EGFR	15
Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation	15
Mechanisms of Translation-coupled Quality Control	15
Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates	15
Structural Basis of DEPTOR to Recognize Phosphatidic Acid Using its Tandem DEP Domains	15
Editorial Board	15
Intrinsic Disorder in Human RNA-Binding Proteins	15
Enzymatic Reactions inside Biological Condensates	15
Transcriptional and Epigenetic Regulation of Gasdermins	15
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	15
Biomolecular Condensates as Novel Antiviral Targets	15
Pyroptosis, and its Role in Central Nervous System Disease	15
BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins	15
Cholesterol-Mediated Clustering of the HIV Fusion Protein gp41 in Lipid Bilayers	15
Conservation and Diversity in Allosteric Fingerprints of Proteins for Evolutionary-inspired Engineering and Design	15