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	386
Mutations Strengthened SARS-CoV-2 Infectivity	369
AlphaFold and Implications for Intrinsically Disordered Proteins	309
Structural insights into SARS-CoV-2 proteins	241
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics	201
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants	179
FunRich enables enrichment analysis of OMICs datasets	146
The AlphaFold Database of Protein Structures: A Biologist’s Guide	130
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die	123
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive	104
Molecular Interactions Between Components of the Circadian Clock and the Immune System	101
The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation	94
Molecular Links between the Circadian Clock and the Cell Cycle	81
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational	80
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition	78
Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau	78
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools	72
Mechanisms of Antiviral Immune Evasion of SARS-CoV-2	68
The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin	67
Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility	67
Structure and Function of Chromatin Remodelers	67
Cation-π Interactions and their Functional Roles in Membrane Proteins	65
Molecular Mechanisms for Bacterial Potassium Homeostasis	64
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation	63
Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition	63

The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks	60
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins	60
SSizer: Determining the Sample Sufficiency for Comparative Biological Study	59
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins	58
Synapsin Condensates Recruit alpha-Synuclein	57
The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction	57
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network	55
GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite	55
Structural Basis of Drug Recognition by the Multidrug Transporter ABCG2	54
Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose	54
The Persistent Question of Potassium Channel Permeation Mechanisms	54
Molecular Strategies Underlying Porphyromonas gingivalis Virulence	54
Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation	53
SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca2+	53
The Protein Folding Problem: The Role of Theory	53
Molecular Mechanism of Nramp-Family Transition Metal Transport	51
Contributions of Histone Variants in Nucleosome Structure and Function	50
Molecular Connections Between Circadian Clocks and Aging	50
On the Potential of Machine Learning to Examine the Relationship Between Sequence, Structure, Dynamics and Function of Intrinsically Disordered Proteins	50
Orchestration of Circadian Timing by Macromolecular Protein Assemblies	49
On the molecular nature of large-pore channels	48
Towards Visual Proteomics at High Resolution	48
Enzymatic Reactions inside Biological Condensates	47
The BioImage Archive – Building a Home for Life-Sciences Microscopy Data	47
Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase	46
DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server	46
Regulatory B cells and T cell Regulation in Cancer	46
iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network	46
Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis	45
Pyroptosis-Induced Inflammation and Tissue Damage	45
The Concept of Coupling in the Mammalian Circadian Clock Network	45
PANoptosis in Viral Infection: The Missing Puzzle Piece in the Cell Death Field	44
Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription	44
Circadian Clocks Make Metabolism Run	44
Community-Wide Experimental Evaluation of the PROSS Stability-Design Method	43
AlphaFold and the amyloid landscape	43
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process	43
Anti-Frameshifting Ligand Active against SARS Coronavirus-2 Is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot	42
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology	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
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)	41
Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils	41
Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins	40
Single-Molecule Force Spectroscopy of Protein Folding	40
Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans	40
Designer Condensates: A Toolkit for the Biomolecular Architect	39
Structural Pharmacology of TRP Channels	39
PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters	39
Regulation of Lytic and Non-Lytic Functions of Gasdermin Pores	38
Pharmacological Interventions to Circadian Clocks and Their Molecular Bases	38

Pyroptosis, and its Role in Central Nervous System Disease	38
Building Structural Models of a Whole Mycoplasma Cell	38
Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures	38
Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies	37
MLCPP 2.0: An Updated Cell-penetrating Peptides and Their Uptake Efficiency Predictor	37
Integrative Structural Biology in the Era of Accurate Structure Prediction	37
Structural Investigations of Full-Length Insulin Receptor Dynamics and Signalling	36
Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase	36
Structure and Mechanism of DHHC Protein Acyltransferases	36
Phosphorylation Timers in the Neurospora crassa Circadian Clock	35
Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design	35
Structural Basis for Activation of the Heterodimeric GABAB Receptor	35
On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies	34
Structural Insights into the Mechanisms and Pharmacology of K2P Potassium Channels	34
Lipid A Phosphoethanolamine Transferase: Regulation, Structure and Immune Response	34
DNA mechanics and its biological impact	34
Structural Pharmacology of Voltage-Gated Sodium Channels	34
ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides	34
Circadian and Sleep Metabolomics Across Species	34
3dRNA: 3D Structure Prediction from Linear to Circular RNAs	33
HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry	33
THRONE: A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites	32
CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation	32
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain	32
Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation	31
CTP-controlled liquid–liquid phase separation of ParB	31
Subtelomeric Transcription and its Regulation	31
Emerging Bioelectronics for Brain Organoid Electrophysiology	31
Molecular Insights into the Architecture of the Human SMC5/6 Complex	31
Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle	30
Mechanistic Insights into Gasdermin Pore Formation and Regulation in Pyroptosis	30
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data	30
Transcription Regulation Through Nascent RNA Folding	30
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit	30
N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins	30
MEDUSA: Prediction of Protein Flexibility from Sequence	30
Proteomics in Circadian Biology	30
What do Transcription Factors Interact With?	29
Dissecting the Functional Contributions of the Intrinsically Disordered C-terminal Tail of Bacillus subtilis FtsZ	29
Silence at the End: How Drosophila Regulates Expression and Transposition of Telomeric Retroelements	29
The Function of Tafazzin, a Mitochondrial Phospholipid–Lysophospholipid Acyltransferase	29
Protofilament Structure and Supramolecular Polymorphism of Aggregated Mutant Huntingtin Exon 1	29
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs	29
Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation	29
Structural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase	28
Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions	28
TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression	28
Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex	28
FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity	28
Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp	28
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes	28
Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases	27
Nucleosome Clutches are Regulated by Chromatin Internal Parameters	27
Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1–42)	27
Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO	27
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements	27
Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations	27
Degradation of Alzheimer’s Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme	27
PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane	26
How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein	26
An atomic model for the human septin hexamer by cryo-EM	26
Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome	26
Archaea: The Final Frontier of Chromatin	26
Current Knowledge and Future Directions in Developing Strategies to Combat Pseudomonas aeruginosa Infection	26
Pyroptosis in Kidney Disease	25
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics	25
TERRA, a Multifaceted Regulator of Telomerase Activity at Telomeres	25
How does RNA fold dynamically?	25
Amplitude Effects Allow Short Jet Lags and Large Seasonal Phase Shifts in Minimal Clock Models	25
Nucleosome Positioning and Spacing: From Mechanism to Function	25
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region	25
Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase	24
The Axial Alignment of Titin on the Muscle Thick Filament Supports Its Role as a Molecular Ruler	24
Centromeric RNA and Its Function at and Beyond Centromeric Chromatin	24
Membrane Shape and the Regulation of Biological Processes	24
A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid	24
Molecular-genetic Manipulation of the Suprachiasmatic Nucleus Circadian Clock	24
AlphaFold – A Personal Perspective on the Impact of Machine Learning	24
Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly	24
Telomeric Chromatin and TERRA	23

Systems Level Understanding of Circadian Integration with Cell Physiology	23
Building Better Barrels – β-barrel Biogenesis and Insertion in Bacteria and Mitochondria	23
Mechanisms and Consequences of Noncanonical Inflammasome-Mediated Pyroptosis	23
Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism	23
Development of the Circadian Core Machinery in Mammals	23
Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models	23
Mechanisms of PI(4,5)P2 Enrichment in HIV-1 Viral Membranes	23
ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations	23
Molecular Recognition at Septin Interfaces: The Switches Hold the Key	23
Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein Dynamics	23
SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1	23
Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes	23
Intrinsic Disorder in Human RNA-Binding Proteins	22
Blue Light-Directed Cell Migration, Aggregation, and Patterning	22
Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa	22
The Proteome Folding Problem and Cellular Proteostasis	22
Biochemical Timekeeping Via Reentrant Phase Transitions	22
Interleukin 35 Regulatory B Cells	22
Translocon-Associated Protein Complex (TRAP) is Crucial for Co-Translational Translocation of Pre-Proinsulin	22
Chemical Modulation of Gasdermin-Mediated Pyroptosis and Therapeutic Potential	22
J-Domain Proteins in Bacteria and Their Viruses	22
ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins	22
Structure of the Human Cholesterol Transporter ABCG1	22
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
Can We AlphaFold Our Way Out of the Next Pandemic?	21
TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites	21
Applications of Genetic Code Expansion in Studying Protein Post-translational Modification	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
Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase	21
A TfR-Binding Cystine-Dense Peptide Promotes Blood–Brain Barrier Penetration of Bioactive Molecules	21
The Structure and Ubiquitin Binding Properties of TRAF RING Heterodimers	21
A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps	21
Protein Phosphatase-1 Complex Disassembly by p97 is Initiated through Multivalent Recognition of Catalytic and Regulatory Subunits by the p97 SEP-domain Adapters	20
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases	20
Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis	20
Disordered Regions Flanking the Binding Interface Modulate Affinity between CBP and NCOA	20
Breaths, Twists, and Turns of Atomistic Nucleosomes	20
Roles of Noncoding RNAs in Ciliate Genome Architecture	20
Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery	20
Nuclear Protein Condensates and Their Properties in Regulation of Gene Expression	20
B cells from Patients with Rheumatoid Arthritis Show Conserved CD39-Mediated Regulatory Function and increased CD39 Expression After Positive Response to Therapy	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
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances	20
Clusters of a Few Bound Cofilins Sever Actin Filaments	20
Orientational Ambiguity in Septin Coiled Coils and its Structural Basis	19
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes	19
Protein Aggregation and Disaggregation in Cells and Development	19
Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand–Receptor Interactions	19
Molecular Regulation of Circadian Chromatin	19
Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions	19
RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining	19
Non-coding RNAs at the Eukaryotic rDNA Locus: RNA–DNA Hybrids and Beyond	19
Spatial organization of Dps and DNA–Dps complexes	19
Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria	19
Structural Changes in Aptamers are Essential for Synthetic Riboswitch Engineering	19
Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids	19
Approaching Neutrophil Pyroptosis	19
The promise of cryo-EM to explore RNA structural dynamics	19
A Light-Oxygen-Voltage Receptor Integrates Light and Temperature	19
Transglutaminase-Mediated Cross-Linking of Tropoelastin to Fibrillin Stabilises the Elastin Precursor Prior to Elastic Fibre Assembly	18
Protein Disulfide Exchange by the Intramembrane Enzymes DsbB, DsbD, and CcdA	18
The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development	18
Deep Enzymology Studies on DNA Methyltransferases Reveal Novel Connections between Flanking Sequences and Enzyme Activity	18
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation	18
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues	18
HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions	18
Targeted Killing of Pseudomonas aeruginosa by Pyocin G Occurs via the Hemin Transporter Hur	18
ClusPro LigTBM: Automated Template-based Small Molecule Docking	18
Applications of Brain Organoids for Infectious Diseases	18
Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes	18
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters	18
The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach	18
Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes	18
Next Generation Protein Structure Predictions and Genetic Variant Interpretation	18
Two Classes of Myosin Inhibitors, Para-nitroblebbistatin and Mavacamten, Stabilize β-Cardiac Myosin in Different Structural and Functional States	18
Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading	18
The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA	17
The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition	17
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation	17
Molecular Connections Between Circadian Clocks and Mood-related Behaviors	17
Simplicity is the Ultimate Sophistication—Crosstalk of Post-translational Modifications on the RNA Polymerase II	17
Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer	17
RAN Translation of the Expanded CAG Repeats in the SCA3 Disease Context	17
Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I	17
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	17
ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities	17
Structural Basis for Silicic Acid Uptake by Higher Plants	17
Continuous Assembly of β-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (RTX) Proteins	17
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53	17
Liquid–Liquid Phase Separation at the Plasma Membrane–Cytosol Interface: Common Players in Adhesion, Motility, and Synaptic Function	17
Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution	17
Pyroptosis in Steatohepatitis and Liver Diseases	16