Proteins-Structure Function and Bioinformatics

Article	Citations
	197
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	183
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	122
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	118
Issue Information ‐ Table of Content	85
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	76
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	73
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	62
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	61
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	57
Molecular dynamics studies of CED ‐4/ CED ‐9/ EGL	55
rrQNet : Protein contact map quality estimation by deep evolutionary reconciliation	46
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	44
Protein structuromics: A new method for protein structure–function crosstalk in glioma	44
Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding	41
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	41
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	36
Oxygen‐insensitive nitroreductase E. coli NfsA , but not NfsB , is inhi	35
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	34
In Silico Characterization of Bromo‐DragonFLY Binding to the 5‐HT2A Receptor: Molecular Insights Into a Potent Designer Psychedelic	33
Issue Information ‐ Table of Content	33
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	32
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein	32
Biochemical, Biophysical, and Mechanistic Insights on a Putative Oxidoreductase From Mycobacterium tuberculosis	28
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	28

Location of S‐nitrosylated cysteines in protein three‐dimensional structures	27
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	27
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	26
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	24
Crystal structure of GTP ‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	24
Cover Image, Volume 94, Issue 1	23
Issue Information ‐ Table of Content	21
Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine	21
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	21
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	21
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	20
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an αββα‐Fold Arrangement	19
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Issue Information ‐ Table of Content	16
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	16
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	16
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	16
The enigmatic HCN channels: A cellular neurophysiology perspective	15
Annexin A1, A2, A5, and A6 involvement in human pathologies	14
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	14
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	14
Mechanistic Insights Into the Inhibition of Dengue Virus NS5 Methyltransferase by Herbacetin	14
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	14
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	13
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	12
Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With	12
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	12
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	12
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	12
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar	12
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	12
Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity	12
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Issue Information ‐ Table of Content	11
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Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	11
Issue Information ‐ Table of Content	11
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	10
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	10
DLPacker : Deep learning for prediction of amino acid side chain conformations in proteins	10
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	10
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae	10
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	10
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	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
Efficient and accurate binding free energy calculation of Aβ 9–40 protofilament propagation	10
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	10
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	10
Biological nanopores for sensing applications	9

Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	9
Issue Information ‐ Table of Content	9
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	9
Graph_RG: Dominating CASP16 's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	9
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	9
Issue Information ‐ Table of Content	9
Tertiary structure assessment at CASP15	9
MPA‐Pred : A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	9
VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	9
Protein Target Highlights in CASP16 : Insights From the Structure Providers	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
Assessment of the assessment—All about complexes	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
Analysis of the crystal structure of a parallel three‐stranded coiled coil	8
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	8
Cross‐linking disulfide bonds govern solution structures of diabodies	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
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	8
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	8
Rational peptide design for targeting cancer cell invasion	8
Cover Image, Volume 93, Issue 12	8
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	8
Exploiting protein language models for the precise classification of ion channels and ion transporters	8
The avidin‐theophylline complex: A structural and computational study	8
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	8
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	8
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	7
The dynamic basis of structural order in proteins	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Issue Information ‐ Forthcoming	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
Energetic and structural insights behind calcium induced conformational transition in calmodulin	7
Issue Information ‐ Table of Content	7
Distinct Substrate and Intermediate Recognition via Mutation Effects on Mycobacterium tuberculosis	7
Editorial: Special issue Transporter and Channel	7
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	7
α/β Hydrolases: Toward Unraveling Entangled Classification	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
Structure and Dynamics of Cannabinoid Binding to the GABA A Receptor	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94  kDa	7
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	7
Based on Molecular Docking, Molecular Dynamics Simulation and MM / PB ( G	7
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	7
Prediction of interactions between cell surface proteins by machine learning	7
Issue Information ‐ Table of Content	7
CRMSNet : A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for	7
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	7
Issue Information ‐ Table of Content	7
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	7
Transmembrane proteins—Different anchoring systems	7
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HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold	6
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	6
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	6
Proteome analysis of the circadian clock protein PERIOD2	6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	6
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Issue Information ‐ Forthcoming	6
Cover Image, Volume 94, Issue 1	6
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	6
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	6
Crystal structure of an L‐type lectin domain from archaea	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
Updates to the CASP Infrastructure in 2024	6
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Plastic structures for diverse substrates: A revisit of human ABC transporters	6
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Dynamical changes of SARS‐CoV ‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
Assessment of three‐dimensional RNA structure prediction in CASP15	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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Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	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
Exploring Compactness and Dynamics of Apomyoglobin	5
What can AlphaFold do for antimicrobial amyloids?	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV ‐2 neutralizing antibodies	5
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
Issue Information ‐ Table of Content	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	5
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Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	5
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The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	5
The Crystal Structure of the Domain of Unknown Function 1480 ( DUF1480 ) From Klebsiella pneumoniae	5
Cover Image, Volume 91, Issue 12	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
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Issue Information ‐ Table of Content	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP ‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	5
The following articles for this Special Issue were published in different Issues	5
Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella	5
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
Cover Image, Volume 93, Issue 11	4
Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	4
Issue Information ‐ Forthcoming	4
SARS‐CoV ‐2 main protease mutation analysis via a kinematic method	4
Issue Information ‐ Table of Content	4
Scaffold Matcher : A CMA‐ES based algorithm for identifying hotspot aligned peptidomimetic scaffol	4
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Protein aggregates thermodynamically order regardless of sequence	4
Protein folding and unfolding: proline cis ‐ trans isomerization at the c	4
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A geometrical framework for thinking about proteins	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory	4
In silico study predicts a key role of RNA ‐binding domains 3 and 4 in nucleolin–miRNA interaction	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	4
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	4
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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
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	4
Structural Implications of HIV ‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	4
AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold ‐Based K	4
Aspergillus oryzae α‐ l ‐rhamnosidase: Crystal structure and insigh	4
Issue Information ‐ Forthcoming	4
DeepUSPS : Deep Learning‐Empowered Unconstrained‐Structural Protein Sequence Design	4
AlphaFold and Docking Approaches for Antibody–Antigen and Other Targets: Insights From CAPRI Rounds 47–55	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	4
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Understanding the Role of RING ‐Between‐ RING E3 Ligase of the Human Malaria Parasite	4
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	4
Challenges in bridging the gap between protein structure prediction and functional interpretation	4
Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	4
Structural Basis for M2 ‐2– MAVS Proteins Interaction in Human Metapneumovirus (	4
Conformational Dynamics and Molecular Characterization of Alsin MORN Monomer and Dimeric Assemblies	4
Issue Information ‐ Table of Content	4
Computational Characterization of the Role of LEM2 / LaminA Interactions on the Stability of	3
The Curious Case of CysE : Diversity and Distribution of Serine Acetyltransferases in Bacteria	3
Structural basis for peptide recognition by archaeal oligopeptide permease A	3
Benchmarking the accuracy of structure‐based binding affinity predictors on Spike–ACE2 deep mutational interaction set	3
GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function	3
II . Geometrical framework for thinking about globular proteins: The power of poking	3
Improving protein structure prediction with extended sequence similarity searches and deep‐learning‐based refinement in CASP15	3
Cover Image, Volume 90, Issue 7	3
Circuit topology predicts pathogenicity of missense mutations	3
Structure of the Complex of Lactoperoxidase With Nitric Oxide at 1.95 Å Resolution	3
Oxidation of active cysteines mediates protein aggregation of S10R, the cataract‐associated mutant of mouse GammaB‐crystallin	3
Rieske Iron–Sulfur Cluster Proteins From an Anaerobic Ammonium Oxidizer Suggest Unusual Energetics in Their Parent Rieske/Cytochrome b Complexes	3
Protein–Protein Interaction Prediction via Structure‐Based Deep Learning	3
The human ribosome‐associated complex suppresses prion formation in yeast	3
Estimation of model accuracy in CASP15 using the ModFOLDdock server	3
Issue Information ‐ Forthcoming	3
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Issue Information ‐ Table of Content	3
Interfacial residues in protein–protein complexes are in the eyes of the beholder	3
On the Variation of Structural Divergence Among Residues in Enzyme Evolution	3
Protein Involved in Initiation 1 Interaction With Starch Synthase 4 From Arabidopsis thaliana Induces Inhibition of Elongating Activity	3
Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in	3
The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation	3
In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein–Protein Interactions	3
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units	3
The high identity of the Trypanosoma cruzi Group‐I of trans‐sialidases points them as promising vaccine immunogens	3
Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	3