Proteins-Structure Function and Bioinformatics

Article	Citations
	441
Issue Information ‐ Forthcoming	351
	170
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	167
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	106
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	93
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	90
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	65
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	63
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	63
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	54
Molecular dynamics studies of CED‐4/CED‐9/EGL‐1 ternary complex reveal CED‐4 release mechanism in the linear apoptotic pathway of Caenorhabditis ele	51
Protein structuromics: A new method for protein structure–function crosstalk in glioma	50
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	48
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	46
Development of a Novel Method for Representing 3D Structures of Nucleotides Using the Concept of the TSR Algorithm and Evaluation of the Method Through Studying Specific Interactions Between DNAs and	40
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	40
SARS‐CoV‐2 neutralizing antibody epitopes are overlapping and highly mutated which raises the chances of escape variants and requires development of broadly reactive vaccines	38
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	34
Issue Information ‐ Table of Content	34
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	34
Issue Information ‐ Forthcoming	32
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	32
Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site‐directed mutagenesis	31
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	30

Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	30
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	29
Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x‐ray reference structures as a prediction benchmark	29
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	28
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	27
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	27
Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions	27
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	25
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	25
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	24
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	23
Issue Information ‐ Table of Content	22
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	22
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	22
Issue Information ‐ Table of Content	22
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zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	20
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	19
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	19
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	18
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	17
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	16
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches	16
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	15
Improving AlphaFold2‐ and AlphaFold3‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP16	15
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	15
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity	15
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an αββα‐Fold Arrangement	14
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	14
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Annexin A1, A2, A5, and A6 involvement in human pathologies	13
Issue Information ‐ Table of Content	13
The enigmatic HCN channels: A cellular neurophysiology perspective	13
Issue Information ‐ Table of Content	12
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	12
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CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	12
Issue Information ‐ Table of Content	12
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	11
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	11
Biological nanopores for sensing applications	11
The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	11
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles	11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	11
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	11
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	10
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	10
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	10
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	10
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	10

Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation	10
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	10
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	10
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	10
Graph_RG: Dominating CASP16's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	10
Tertiary structure assessment at CASP15	10
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments	10
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	9
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	9
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	9
The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling	9
Issue Information ‐ Table of Content	9
Analysis of the crystal structure of a parallel three‐stranded coiled coil	9
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	9
Assessment of the assessment—All about complexes	9
Issue Information ‐ Table of Content	9
The amyloid concentric β‐barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels	9
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	8
Rational peptide design for targeting cancer cell invasion	8
Prediction of interactions between cell surface proteins by machine learning	8
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	8
Editorial: Special issue Transporter and Channel	8
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	8
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	8
α/β Hydrolases: Toward Unraveling Entangled Classification	8
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	8
Low‐frequency collective motion of DNA‐binding domain defines p53 function	8
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	8
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	8
The avidin‐theophylline complex: A structural and computational study	8
The dynamic basis of structural order in proteins	8
Assessing the accuracy of contact and distance predictions in CASP14	8
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	8
Exploiting protein language models for the precise classification of ion channels and ion transporters	8
Issue Information ‐ Forthcoming	7
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	7
Cross‐linking disulfide bonds govern solution structures of diabodies	7
Issue Information ‐ Table of Content	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Cover Image, Volume 90, Issue 1	7
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	7
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	7
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp4	7
Issue Information ‐ Table of Content	7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
Transmembrane proteins—Different anchoring systems	7
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	7
Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α	7
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	7
Structural Classification Insights Into the Plant Defensive Peptides	7
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	7
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
Assessment of three‐dimensional RNA structure prediction in CASP15	6
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
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Cover Image, Volume 89, Issue 11	6
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	6
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes	6
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Issue Information ‐ Table of Content	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	6
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CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	6

Exploring Compactness and Dynamics of Apomyoglobin	6
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Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	6
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Crystal structure of an L‐type lectin domain from archaea	6
Issue Information ‐ Forthcoming	6
Proteome analysis of the circadian clock protein PERIOD2	6
Energetic and structural insights behind calcium induced conformational transition in calmodulin	6
Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	6
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Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
What can AlphaFold do for antimicrobial amyloids?	5
Issue Information ‐ Table of Content	5
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	5
Cover Image, Volume 91, Issue 12	5
Protein aggregates thermodynamically order regardless of sequence	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Issue Information ‐ Table of Content	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies	5
ScaffoldMatcher:A CMA‐ESbased algorithm for identifying hotspot aligned peptidomimetic scaffolds	5
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
The following articles for this Special Issue were published in different Issues	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Atomistic insight into the luminal allosteric regulation of vesicular glutamate transporter 2 by chloride and protons: An all‐atom molecular dynamics simulation study	5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	5