Journal of Molecular Biology

Article	Citations
Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop	385
Mutations Strengthened SARS-CoV-2 Infectivity	368
AlphaFold and Implications for Intrinsically Disordered Proteins	303
Structural insights into SARS-CoV-2 proteins	238
Autophagy in Parkinson's Disease	201
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics	191
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants	178
Autophagosome-Lysosome Fusion	175
Autophagy Induction as a Therapeutic Strategy for Neurodegenerative Diseases	153
FunRich enables enrichment analysis of OMICs datasets	140
The AlphaFold Database of Protein Structures: A Biologist’s Guide	126
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	115
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive	100
Molecular Interactions Between Components of the Circadian Clock and the Immune System	94
The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation	90
Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau	77
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational	76
Molecular Links between the Circadian Clock and the Cell Cycle	74
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	74
Integrative Modelling of Biomolecular Complexes	69
Mechanisms of Antiviral Immune Evasion of SARS-CoV-2	68
Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility	66
The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin	65
Structure and Function of Chromatin Remodelers	64
The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators	63

Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition	63
Cation-π Interactions and their Functional Roles in Membrane Proteins	61
Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS)	61
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools	59
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation	59
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins	58
SSizer: Determining the Sample Sufficiency for Comparative Biological Study	58
The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks	58
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	56
Molecular Mechanisms for Bacterial Potassium Homeostasis	56
Synapsin Condensates Recruit alpha-Synuclein	55
The Persistent Question of Potassium Channel Permeation Mechanisms	54
Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose	53
Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation	53
The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction	53
SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca2+	53
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	53
GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite	53
Structural Basis of Drug Recognition by the Multidrug Transporter ABCG2	52
Molecular Strategies Underlying Porphyromonas gingivalis Virulence	52
Ubiquitin and Receptor-Dependent Mitophagy Pathways and Their Implication in Neurodegeneration	52
Autophagy and Protein Secretion	50
The Protein Folding Problem: The Role of Theory	50
Selective Autophagy Receptors in Neuronal Health and Disease	50
On the Potential of Machine Learning to Examine the Relationship Between Sequence, Structure, Dynamics and Function of Intrinsically Disordered Proteins	50
Molecular Mechanism of Nramp-Family Transition Metal Transport	49
Molecular Connections Between Circadian Clocks and Aging	48
Contributions of Histone Variants in Nucleosome Structure and Function	48
Orchestration of Circadian Timing by Macromolecular Protein Assemblies	47
DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server	46
Towards Visual Proteomics at High Resolution	45
iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network	45
Enzymatic Reactions inside Biological Condensates	45
Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase	45
Autophagy in Astrocytes and its Implications in Neurodegeneration	44
Circadian Clocks Make Metabolism Run	44
Pyroptosis-Induced Inflammation and Tissue Damage	44
The BioImage Archive – Building a Home for Life-Sciences Microscopy Data	44
The Concept of Coupling in the Mammalian Circadian Clock Network	44
On the molecular nature of large-pore channels	43
Regulatory B cells and T cell Regulation in Cancer	43
The Synaptic Autophagy Cycle	43
PANoptosis in Viral Infection: The Missing Puzzle Piece in the Cell Death Field	43
Impairment of Lysosome Function and Autophagy in Rare Neurodegenerative Diseases	43
AlphaFold and the amyloid landscape	42
Anti-Frameshifting Ligand Active against SARS Coronavirus-2 Is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot	42
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process	42
Disulfide Bonds Play a Critical Role in the Structure and Function of the Receptor-binding Domain of the SARS-CoV-2 Spike Antigen	42
Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis	42
Community-Wide Experimental Evaluation of the PROSS Stability-Design Method	42

Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription	41
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology	41
Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils	40
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)	40
Designer Condensates: A Toolkit for the Biomolecular Architect	39
Single-Molecule Force Spectroscopy of Protein Folding	39
Regulation of Lytic and Non-Lytic Functions of Gasdermin Pores	38
Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans	38
Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures	38
PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters	38
Pyroptosis, and its Role in Central Nervous System Disease	37
Autophagy as a Cellular Stress Response Mechanism in the Nervous System	37
Building Structural Models of a Whole Mycoplasma Cell	37
Pharmacological Interventions to Circadian Clocks and Their Molecular Bases	37
Structural Pharmacology of TRP Channels	37
Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins	36
MLCPP 2.0: An Updated Cell-penetrating Peptides and Their Uptake Efficiency Predictor	36
Structure and Mechanism of DHHC Protein Acyltransferases	36
Autophagosome Biogenesis Machinery	36
Integrative Structural Biology in the Era of Accurate Structure Prediction	35
Structural Investigations of Full-Length Insulin Receptor Dynamics and Signalling	35
Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase	35
Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies	34
Circadian and Sleep Metabolomics Across Species	34
Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design	34
Phosphorylation Timers in the Neurospora crassa Circadian Clock	34
HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry	33
Structural Basis for Activation of the Heterodimeric GABAB Receptor	33
ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides	33
On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies	32
DNA mechanics and its biological impact	32
Structural Pharmacology of Voltage-Gated Sodium Channels	31
THRONE: A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites	31
Lipid A Phosphoethanolamine Transferase: Regulation, Structure and Immune Response	31
Structural Insights into the Mechanisms and Pharmacology of K2P Potassium Channels	31
MEDUSA: Prediction of Protein Flexibility from Sequence	30
3dRNA: 3D Structure Prediction from Linear to Circular RNAs	30
Subtelomeric Transcription and its Regulation	30
Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle	30
Transcription Regulation Through Nascent RNA Folding	30
Proteomics in Circadian Biology	30
Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation	30
Molecular Insights into the Architecture of the Human SMC5/6 Complex	30
Emerging Bioelectronics for Brain Organoid Electrophysiology	30
Mechanistic Insights into Gasdermin Pore Formation and Regulation in Pyroptosis	30
CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation	30
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	30
Silence at the End: How Drosophila Regulates Expression and Transposition of Telomeric Retroelements	29
Dissecting the Functional Contributions of the Intrinsically Disordered C-terminal Tail of Bacillus subtilis FtsZ	29
N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins	29
CTP-controlled liquid–liquid phase separation of ParB	28
Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex	28
Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation	28
FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity	28
Protofilament Structure and Supramolecular Polymorphism of Aggregated Mutant Huntingtin Exon 1	28
TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression	28
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes	28
Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp	27
The Function of Tafazzin, a Mitochondrial Phospholipid–Lysophospholipid Acyltransferase	27
Structural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase	27
Nucleosome Clutches are Regulated by Chromatin Internal Parameters	27
Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO	27
Degradation of Alzheimer’s Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme	27
Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution	27
Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1–42)	27
Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases	27
Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different	26
Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations	26
Archaea: The Final Frontier of Chromatin	26
Current Knowledge and Future Directions in Developing Strategies to Combat Pseudomonas aeruginosa Infection	26
An atomic model for the human septin hexamer by cryo-EM	26
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data	26
PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane	26
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements	26
What do Transcription Factors Interact With?	26
Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A	26
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	26
Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions	26
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit	25
Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome	25

TERRA, a Multifaceted Regulator of Telomerase Activity at Telomeres	25
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	25
How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein	25
Lowering Mutant Huntingtin Levels and Toxicity: Autophagy-Endolysosome Pathways in Huntington's Disease	25
Integrative/Hybrid Modeling Approaches for Studying Biomolecules	25
Nucleosome Positioning and Spacing: From Mechanism to Function	24
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region	24
Amplitude Effects Allow Short Jet Lags and Large Seasonal Phase Shifts in Minimal Clock Models	24
Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly	24
AlphaFold – A Personal Perspective on the Impact of Machine Learning	24
Centromeric RNA and Its Function at and Beyond Centromeric Chromatin	24
Molecular-genetic Manipulation of the Suprachiasmatic Nucleus Circadian Clock	23
Membrane Shape and the Regulation of Biological Processes	23
Pharmacological Tools to Modulate Autophagy in Neurodegenerative Diseases	23
Autophagy in Rare (NonLysosomal) Neurodegenerative Diseases	23
Mechanisms of PI(4,5)P2 Enrichment in HIV-1 Viral Membranes	23
Telomeric Chromatin and TERRA	23
Systems Level Understanding of Circadian Integration with Cell Physiology	23
SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1	23
β2-adrenergic Agonists Rescue Lysosome Acidification and Function in PSEN1 Deficiency by Reversing Defective ER-to-lysosome Delivery of ClC-7	23
Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase	23
Pyroptosis in Kidney Disease	23
Molecular Recognition at Septin Interfaces: The Switches Hold the Key	23
Development of the Circadian Core Machinery in Mammals	23
A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid	23
ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations	22
Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism	22
Building Better Barrels – β-barrel Biogenesis and Insertion in Bacteria and Mitochondria	22
Conditional Disorder in Small Heat-shock Proteins	22
Biochemical Timekeeping Via Reentrant Phase Transitions	22
Interleukin 35 Regulatory B Cells	22
Chemical Modulation of Gasdermin-Mediated Pyroptosis and Therapeutic Potential	22
The Proteome Folding Problem and Cellular Proteostasis	22
How does RNA fold dynamically?	22
Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes	22
Translocon-Associated Protein Complex (TRAP) is Crucial for Co-Translational Translocation of Pre-Proinsulin	22
Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa	22
Structure of the Human Cholesterol Transporter ABCG1	22
Intrinsic Disorder in Human RNA-Binding Proteins	22
Mechanisms and Consequences of Noncanonical Inflammasome-Mediated Pyroptosis	21
Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations	21
N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 Mpro Dimer	21
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic	21
Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity	21
Blue Light-Directed Cell Migration, Aggregation, and Patterning	21
TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites	21
Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein Dynamics	21
Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models	21
A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps	21
Applications of Genetic Code Expansion in Studying Protein Post-translational Modification	21
A TfR-Binding Cystine-Dense Peptide Promotes Blood–Brain Barrier Penetration of Bioactive Molecules	21
The Axial Alignment of Titin on the Muscle Thick Filament Supports Its Role as a Molecular Ruler	21
Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase	20
Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery	20
The Structure and Ubiquitin Binding Properties of TRAF RING Heterodimers	20
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	20
Disordered Regions Flanking the Binding Interface Modulate Affinity between CBP and NCOA	20
J-Domain Proteins in Bacteria and Their Viruses	20
PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning	20
Mechanistic Inferences From Analysis of Measurements of Protein Phase Transitions in Live Cells	20
ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins	20
Protein Phosphatase-1 Complex Disassembly by p97 is Initiated through Multivalent Recognition of Catalytic and Regulatory Subunits by the p97 SEP-domain Adapters	20
Can We AlphaFold Our Way Out of the Next Pandemic?	20
Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions	19
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	19
Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand–Receptor Interactions	19
Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria	19
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	19
Non-coding RNAs at the Eukaryotic rDNA Locus: RNA–DNA Hybrids and Beyond	19
B cells from Patients with Rheumatoid Arthritis Show Conserved CD39-Mediated Regulatory Function and increased CD39 Expression After Positive Response to Therapy	19
Roles of Noncoding RNAs in Ciliate Genome Architecture	19
Orientational Ambiguity in Septin Coiled Coils and its Structural Basis	19
Approaching Neutrophil Pyroptosis	19
The pROS of Autophagy in Neuronal Health	19
Breaths, Twists, and Turns of Atomistic Nucleosomes	19
Deep Enzymology Studies on DNA Methyltransferases Reveal Novel Connections between Flanking Sequences and Enzyme Activity	18
Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes	18
Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis	18
Protein Disulfide Exchange by the Intramembrane Enzymes DsbB, DsbD, and CcdA	18
Molecular Regulation of Circadian Chromatin	18
Next Generation Protein Structure Predictions and Genetic Variant Interpretation	18
Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids	18
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters	18
Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes	18
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	18
Pathomechanism Heterogeneity in the Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Disease Spectrum: Providing Focus Through the Lens of Autophagy	18
Nuclear Protein Condensates and Their Properties in Regulation of Gene Expression	18
Clusters of a Few Bound Cofilins Sever Actin Filaments	18
A Light-Oxygen-Voltage Receptor Integrates Light and Temperature	18
Targeted Killing of Pseudomonas aeruginosa by Pyocin G Occurs via the Hemin Transporter Hur	17
ClusPro LigTBM: Automated Template-based Small Molecule Docking	17
Spatial organization of Dps and DNA–Dps complexes	17
Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution	17
Molecular Connections Between Circadian Clocks and Mood-related Behaviors	17
Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes	17