Journal of Molecular Biology

Papers
(The TQCC of Journal of Molecular Biology is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)
ArticleCitations
AlphaFold and Implications for Intrinsically Disordered Proteins356
Structural insights into SARS-CoV-2 proteins260
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics246
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants182
Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die177
FunRich enables enrichment analysis of OMICs datasets176
The AlphaFold Database of Protein Structures: A Biologist’s Guide161
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive132
The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation115
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools112
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational101
Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition89
Structure and Function of Chromatin Remodelers87
Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau85
Molecular Mechanisms for Bacterial Potassium Homeostasis82
Cation-π Interactions and their Functional Roles in Membrane Proteins81
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation79
The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin78
Synapsin Condensates Recruit alpha-Synuclein75
Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility74
Mechanisms of Antiviral Immune Evasion of SARS-CoV-272
The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction68
Molecular Strategies Underlying Porphyromonas gingivalis Virulence68
The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins67
GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite67
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins66
Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition65
The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network64
SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca2+61
The Protein Folding Problem: The Role of Theory61
Contributions of Histone Variants in Nucleosome Structure and Function61
On the Potential of Machine Learning to Examine the Relationship Between Sequence, Structure, Dynamics and Function of Intrinsically Disordered Proteins60
The Persistent Question of Potassium Channel Permeation Mechanisms60
Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis59
Structural Basis of Drug Recognition by the Multidrug Transporter ABCG258
Uncovering Non-random Binary Patterns Within Sequences of Intrinsically Disordered Proteins58
On the molecular nature of large-pore channels57
Molecular Mechanism of Nramp-Family Transition Metal Transport57
The BioImage Archive – Building a Home for Life-Sciences Microscopy Data57
Enzymatic Reactions inside Biological Condensates56
Regulatory B cells and T cell Regulation in Cancer56
Pyroptosis-Induced Inflammation and Tissue Damage56
iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network54
Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription54
Towards Visual Proteomics at High Resolution53
PANoptosis in Viral Infection: The Missing Puzzle Piece in the Cell Death Field52
Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)50
AlphaFold and the amyloid landscape50
MLCPP 2.0: An Updated Cell-penetrating Peptides and Their Uptake Efficiency Predictor48
Single-Molecule Force Spectroscopy of Protein Folding47
Structural Insights into the Mechanisms and Pharmacology of K2P Potassium Channels47
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process47
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology47
Community-Wide Experimental Evaluation of the PROSS Stability-Design Method46
Disulfide Bonds Play a Critical Role in the Structure and Function of the Receptor-binding Domain of the SARS-CoV-2 Spike Antigen46
Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures46
PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters45
Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils45
3dRNA: 3D Structure Prediction from Linear to Circular RNAs45
Pyroptosis, and its Role in Central Nervous System Disease45
Regulation of Lytic and Non-Lytic Functions of Gasdermin Pores43
Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans43
Structural Pharmacology of TRP Channels43
Building Structural Models of a Whole Mycoplasma Cell42
Structural Pharmacology of Voltage-Gated Sodium Channels42
Emerging Bioelectronics for Brain Organoid Electrophysiology42
CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation42
THRONE: A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites41
Designer Condensates: A Toolkit for the Biomolecular Architect41
Structural Investigations of Full-Length Insulin Receptor Dynamics and Signalling40
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit40
Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies39
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data39
DNA mechanics and its biological impact39
Structural Basis for Activation of the Heterodimeric GABAB Receptor39
CTP-controlled liquid–liquid phase separation of ParB39
Integrative Structural Biology in the Era of Accurate Structure Prediction39
N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins38
MEDUSA: Prediction of Protein Flexibility from Sequence37
What do Transcription Factors Interact With?36
Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation36
Co-Translational Folding of the First Transmembrane Domain of ABC-Transporter CFTR is Supported by Assembly with the First Cytosolic Domain35
On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies35
How does RNA fold dynamically?34
Transcription Regulation Through Nascent RNA Folding34
Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle34
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs34
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes33
The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region33
Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases33
Mechanistic Insights into Gasdermin Pore Formation and Regulation in Pyroptosis32
Nucleosome Clutches are Regulated by Chromatin Internal Parameters32
An atomic model for the human septin hexamer by cryo-EM32
Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions32
Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics32
Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome32
FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity31
How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein31
Pyroptosis in Kidney Disease31
Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models31
Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein Dynamics30
Archaea: The Final Frontier of Chromatin30
Structural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase30
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements30
SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP129
ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations29
PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning29
Degradation of Alzheimer’s Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme29
Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations28
Building Better Barrels – β-barrel Biogenesis and Insertion in Bacteria and Mitochondria28
Phase Separation in Biology and Disease; Current Perspectives and Open Questions28
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances28
Interleukin 35 Regulatory B Cells28
Nucleosome Positioning and Spacing: From Mechanism to Function28
Applications of Genetic Code Expansion in Studying Protein Post-translational Modification27
Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly27
N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 Mpro Dimer27
The promise of cryo-EM to explore RNA structural dynamics27
Can We AlphaFold Our Way Out of the Next Pandemic?26
ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins26
Biochemical Timekeeping Via Reentrant Phase Transitions26
Intrinsic Disorder in Human RNA-Binding Proteins26
CavityPlus 2022 Update: An Integrated Platform for Comprehensive Protein Cavity Detection and Property Analyses with User-friendly Tools and Cavity Databases26
Two Classes of Myosin Inhibitors, Para-nitroblebbistatin and Mavacamten, Stabilize β-Cardiac Myosin in Different Structural and Functional States25
The Proteome Folding Problem and Cellular Proteostasis25
Nuclear Protein Condensates and Their Properties in Regulation of Gene Expression25
Breaths, Twists, and Turns of Atomistic Nucleosomes25
Applications of Brain Organoids for Infectious Diseases25
Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery25
Mechanisms and Consequences of Noncanonical Inflammasome-Mediated Pyroptosis25
Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism24
Protein Aggregation and Disaggregation in Cells and Development24
Protein Phosphatase-1 Complex Disassembly by p97 is Initiated through Multivalent Recognition of Catalytic and Regulatory Subunits by the p97 SEP-domain Adapters24
Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation24
Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions24
Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa24
Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases24
Functional and Pathological Effects of α-Synuclein on Synaptic SNARE Complexes24
AlphaFold – A Personal Perspective on the Impact of Machine Learning24
Disordered Regions Flanking the Binding Interface Modulate Affinity between CBP and NCOA24
Mechanistic Inferences From Analysis of Measurements of Protein Phase Transitions in Live Cells23
Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids23
Chemical Modulation of Gasdermin-Mediated Pyroptosis and Therapeutic Potential23
The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development23
Structural Changes in Aptamers are Essential for Synthetic Riboswitch Engineering23
Orientational Ambiguity in Septin Coiled Coils and its Structural Basis23
Translocon-Associated Protein Complex (TRAP) is Crucial for Co-Translational Translocation of Pre-Proinsulin23
Structure of the Human Cholesterol Transporter ABCG123
TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites23
Next Generation Protein Structure Predictions and Genetic Variant Interpretation23
Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis23
A Light-Oxygen-Voltage Receptor Integrates Light and Temperature23
In vivo Profiling of the Alk Proximitome in the Developing Drosophila Brain22
Common Mechanisms Underlying α-Synuclein-Induced Mitochondrial Dysfunction in Parkinson’s Disease22
RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining22
Simplicity is the Ultimate Sophistication—Crosstalk of Post-translational Modifications on the RNA Polymerase II22
Structural Mechanisms of Mitochondrial Quality Control Mediated by PINK1 and Parkin22
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues22
Clusters of a Few Bound Cofilins Sever Actin Filaments22
Pyroptosis in Steatohepatitis and Liver Diseases22
Deep Enzymology Studies on DNA Methyltransferases Reveal Novel Connections between Flanking Sequences and Enzyme Activity22
Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic22
Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria22
The Structure and Ubiquitin Binding Properties of TRAF RING Heterodimers21
Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes21
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p5321
Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes20
Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases20
B cells from Patients with Rheumatoid Arthritis Show Conserved CD39-Mediated Regulatory Function and increased CD39 Expression After Positive Response to Therapy20
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 Koh20
The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA20
Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes20
Identification and Characterization of the Interaction Between the Methyl-7-Guanosine Cap Maturation Enzyme RNMT and the Cap-Binding Protein eIF4E20
Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation20
Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids20
The Core Complex of the Ca2+-Triggered Presynaptic Fusion Machinery20
Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading20
Approaching Neutrophil Pyroptosis19
HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions19
Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity19
Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation19
Structural Basis for Silicic Acid Uptake by Higher Plants19
RAN Translation of the Expanded CAG Repeats in the SCA3 Disease Context19
Better Cryo-EM Specimen Preparation: How to Deal with the Air–Water Interface?19
Spatial organization of Dps and DNA–Dps complexes19
ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities19
The Nt17 Domain and its Helical Conformation Regulate the Aggregation, Cellular Properties and Neurotoxicity of Mutant Huntingtin Exon 119
The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach19
Modeling Developmental Brain Diseases Using Human Pluripotent Stem Cells-Derived Brain Organoids – Progress and Perspective19
Structure and the Mode of Activity of Lon Proteases from Diverse Organisms19
Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-0730481418
Liquid–Liquid Phase Separation at the Plasma Membrane–Cytosol Interface: Common Players in Adhesion, Motility, and Synaptic Function18
Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution18
The Intrinsically Disordered Proteins MLLT3 (AF9) and MLLT1 (ENL) – Multimodal Transcriptional Switches With Roles in Normal Hematopoiesis, MLL Fusion Leukemia, and Kidney Cancer18
Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences18
Novel LRR-ROC Motif That Links the N- and C-terminal Domains in LRRK2 Undergoes an Order–Disorder Transition Upon Activation18
Gasdermin D and Beyond – Gasdermin-mediated Pyroptosis in Bacterial Infections18
Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation18
High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters18
Accurate Prediction of Protein Thermodynamic Stability Changes upon Residue Mutation using Free Energy Perturbation18
MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation18
Small Molecule Sequestration of the Intrinsically Disordered Protein, p27Kip1, Within Soluble Oligomers18
CpG Islands Shape the Epigenome Landscape18
Liquid-liquid Phase Separation in Viral Function17
Principles of Alternating Access in Multidrug and Toxin Extrusion (MATE) Transporters17
Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization17
MPTherm-pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins17
Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis17
Inhibition of SARS-CoV-2 Infection by Human Defensin HNP1 and Retrocyclin RC-10117
Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile17
Strain Identification and Quantitative Analysis in Microbial Communities17
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data17
Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer17
The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array17
Recent Advances in the Structural Biology of Mg2+ Channels and Transporters17
HSP70, a Novel Regulatory Molecule in B Cell-Mediated Suppression of Autoimmune Diseases17
Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates17
Transcriptional and Epigenetic Regulation of Gasdermins17
Conformational Dynamics Allows Sampling of an “Active-like” State by Oncogenic K-Ras-GDP17
Hofmeister Ions Modulate the Autocatalytic Amyloidogenesis of an Intrinsically Disordered Functional Amyloid Domain via Unusual Biphasic Kinetics17
Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity17
Mapping Electromechanical Coupling Pathways in Voltage-Gated Ion Channels: Challenges and the Way Forward17
PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions17
Genetic Code Expansion Through Quadruplet Codon Decoding17
Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo17
Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications16
Two Bacterial Small Heat Shock Proteins, IbpA and IbpB, Form a Functional Heterodimer16
Plasma Cells: From Cytokine Production to Regulation in Experimental Autoimmune Encephalomyelitis16
Charge Segregation in the Intrinsically Disordered Region Governs VRN1 and DNA Liquid-like Phase Separation Robustness16
AlphaFold: A Special Issue and A Special Time for Protein Science16
Epithelial Pyroptosis in Host Defense16
Towards a ‘Spot On’ Understanding of Transcription in the Nucleus16
TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow16
BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins16
Molecular Mechanisms of Cellular Senescence in Neurodegenerative Diseases16
Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure16
The Role of α-Synuclein in SNARE-mediated Synaptic Vesicle Fusion16
Effects of N-terminal Acetylation on the Aggregation of Disease-related α-synuclein Variants16
Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain16
The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome16
Fidelity of Ribonucleotide Incorporation by the SARS-CoV-2 Replication Complex16
Quantifying the Monomer–Dimer Equilibrium of Tubulin with Mass Photometry16
The Interplay Between Disordered Regions in RNAs and Proteins Modulates Interactions Within Stress Granules and Processing Bodies16
An Eight Amino Acid Segment Controls Oligomerization and Preferred Conformation of the two Non-visual Arrestins16
rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling16
Inflammasomes in T cells16
Regulation of E. coli Rep helicase activity by PriC16
miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples16
Unorthodox Mechanisms to Initiate Translation Open Novel Paths for Gene Expression15
N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins15
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