Proteins-Structure Function and Bioinformatics

Article	Citations
	190
Issue Information ‐ Forthcoming	179
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	118
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	114
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	82
Protein structuromics: A new method for protein structure–function crosstalk in glioma	74
Issue Information ‐ Table of Content	69
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	60
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	59
Oxygen‐insensitive nitroreductase E. coli NfsA , but not NfsB , is inhi	56
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	54
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	45
rrQNet : Protein contact map quality estimation by deep evolutionary reconciliation	44
Molecular dynamics studies of CED ‐4/ CED ‐9/ EGL	42
Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding	38
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	37
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	36
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	34
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	33
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	32
Issue Information ‐ Table of Content	31
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	30
In Silico Characterization of Bromo‐DragonFLY Binding to the 5‐HT2A Receptor: Molecular Insights Into a Potent Designer Psychedelic	30
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	28
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein	26

Location of S‐nitrosylated cysteines in protein three‐dimensional structures	26
Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine	26
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	25
Crystal structure of GTP ‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	24
Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x‐ray reference structures as a prediction b	23
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	23
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	21
Issue Information ‐ Table of Content	21
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	20
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	20
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an αββα‐Fold Arrangement	19
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	18
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Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With	16
Issue Information ‐ Table of Content	16
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	15
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	14
Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity	14
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	14
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar	14
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	13
The enigmatic HCN channels: A cellular neurophysiology perspective	13
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	13
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	13
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	12
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	12
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	12
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	12
Annexin A1, A2, A5, and A6 involvement in human pathologies	12
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	12
Issue Information ‐ Table of Content	11
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CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	11
Issue Information ‐ Table of Content	11
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VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	10
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
MPA‐Pred : A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	10
The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	10
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	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
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	10
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	10
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	10
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae	9
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	9
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	9

Issue Information ‐ Table of Content	9
DLPacker : Deep learning for prediction of amino acid side chain conformations in proteins	9
Protein Target Highlights in CASP16 : Insights From the Structure Providers	9
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	9
Biological nanopores for sensing applications	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
Efficient and accurate binding free energy calculation of Aβ 9–40 protofilament propagation	9
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	9
Issue Information ‐ Table of Content	9
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	9
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	8
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	8
Exploiting protein language models for the precise classification of ion channels and ion transporters	8
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	8
Cross‐linking disulfide bonds govern solution structures of diabodies	8
Assessment of the assessment—All about complexes	8
The avidin‐theophylline complex: A structural and computational study	8
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	8
Cover Image, Volume 93, Issue 12	8
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	8
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	8
Analysis of the crystal structure of a parallel three‐stranded coiled coil	8
Rational peptide design for targeting cancer cell invasion	8
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	8
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	8
Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α	8
Structure and Dynamics of Cannabinoid Binding to the GABA A Receptor	7
CRMSNet : A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for	7
Based on Molecular Docking, Molecular Dynamics Simulation and MM / PB ( G	7
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	7
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	7
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	7
Issue Information ‐ Table of Content	7
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Issue Information ‐ Table of Content	7
Prediction of interactions between cell surface proteins by machine learning	7
The dynamic basis of structural order in proteins	7
α/β Hydrolases: Toward Unraveling Entangled Classification	7
Cover Image, Volume 90, Issue 1	7
Issue Information ‐ Forthcoming	7
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Editorial: Special issue Transporter and Channel	7
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	7
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	7
Transmembrane proteins—Different anchoring systems	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Dynamical changes of SARS‐CoV ‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	6
Issue Information ‐ Forthcoming	6
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Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	6
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94  kDa	6
Updates to the CASP Infrastructure in 2024	6
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	6
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
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TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Assessment of three‐dimensional RNA structure prediction in CASP15	6
Crystal structure of an L‐type lectin domain from archaea	6
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Issue Information ‐ Table of Content	6
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	6
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
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Plastic structures for diverse substrates: A revisit of human ABC transporters	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
Energetic and structural insights behind calcium induced conformational transition in calmodulin	6

Proteome analysis of the circadian clock protein PERIOD2	6
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
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Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV ‐2 neutralizing antibodies	5
The following articles for this Special Issue were published in different Issues	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
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Atomistic insight into the luminal allosteric regulation of vesicular glutamate transporter 2 by chloride and protons: An all‐atom molecular dynamics simulation study	5
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
The Crystal Structure of the Domain of Unknown Function 1480 ( DUF1480 ) From Klebsiella pneumoniae	5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP ‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	5
Issue Information ‐ Table of Content	5
Issue Information ‐ Table of Content	5
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Exploring Compactness and Dynamics of Apomyoglobin	5
What can AlphaFold do for antimicrobial amyloids?	5
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF	5
Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella	5
Cover Image, Volume 91, Issue 12	5
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	5
Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	4
Scaffold Matcher : A CMA‐ES based algorithm for identifying hotspot aligned peptidomimetic scaffol	4
Protein aggregates thermodynamically order regardless of sequence	4
Issue Information ‐ Forthcoming	4
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Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn (	4
Structural Basis for M2 ‐2– MAVS Proteins Interaction in Human Metapneumovirus (	4
DeepUSPS : Deep Learning‐Empowered Unconstrained‐Structural Protein Sequence Design	4
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	4
Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
In silico study predicts a key role of RNA ‐binding domains 3 and 4 in nucleolin–miRNA interaction	4
Issue Information ‐ Forthcoming	4
Cover Image, Volume 93, Issue 11	4
Issue Information ‐ Table of Content	4
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Understanding the Role of RING ‐Between‐ RING E3 Ligase of the Human Malaria Parasite	4
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	4
Challenges in bridging the gap between protein structure prediction and functional interpretation	4
AlphaFold and Docking Approaches for Antibody–Antigen and Other Targets: Insights From CAPRI Rounds 47–55	4
Conformational Dynamics and Molecular Characterization of Alsin MORN Monomer and Dimeric Assemblies	4
A geometrical framework for thinking about proteins	4
Deciphering the role of the two conserved motifs of the ECF41 family σ factor in the autoregulation of its own promoter in Azospirillum brasilense Sp245	4
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory	4
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	4
Aspergillus oryzae α‐ l ‐rhamnosidase: Crystal structure and insigh	4
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Protein folding and unfolding: proline cis ‐ trans isomerization at the c	4
Structural Implications of HIV ‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	4
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	4
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Issue Information ‐ Table of Content	4
Role of Extracellular Histidine Residues for the Function and pH Sensitivity of Human Organic Anion Transporting Polypeptide	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold ‐Based K	4
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
SARS‐CoV ‐2 main protease mutation analysis via a kinematic method	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	4
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