Proteins-Structure Function and Bioinformatics

Article	Citations
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	366
	187
Issue Information ‐ Forthcoming	176
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	109
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	107
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	76
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	69
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	68
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	58
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	57
Issue Information ‐ Table of Content	55
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	53
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	43
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	41
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	39
Protein structuromics: A new method for protein structure–function crosstalk in glioma	35
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	34
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	34
Issue Information ‐ Forthcoming	33
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	33
Issue Information ‐ Table of Content	32
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	31
In Silico Characterization of Bromo‐DragonFLY Binding to the 5‐HT2A Receptor: Molecular Insights Into a Potent Designer Psychedelic	30
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	26

Surveying nonvisual arrestins reveals allosteric interactions between functional sites	25
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	25
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	25
Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions	23
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	23
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	22
Issue Information ‐ Table of Content	21
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	21
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	20
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity	19
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	19
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	19
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	16
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	16
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an αββα‐Fold Arrangement	16
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	15
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	15
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	14
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	14
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches	14
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Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	14
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	13
Issue Information ‐ Table of Content	13
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	12
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Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	12
Improving AlphaFold2‐ and AlphaFold3‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP16	12
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	12
Annexin A1, A2, A5, and A6 involvement in human pathologies	12
The enigmatic HCN channels: A cellular neurophysiology perspective	12
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	11
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Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	11
Issue Information ‐ Table of Content	11
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	11
Issue Information ‐ Table of Content	11
The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	10
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	10
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	10
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments	10
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	10
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	10
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Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation	10
Graph_RG: Dominating CASP16's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	10
Protein Target Highlights in CASP16: Insights From the Structure Providers	9
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	9
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	9
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	9

In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	9
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	9
Biological nanopores for sensing applications	9
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	9
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	9
Tertiary structure assessment at CASP15	9
Exploiting protein language models for the precise classification of ion channels and ion transporters	8
Issue Information ‐ Table of Content	8
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	8
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	8
Analysis of the crystal structure of a parallel three‐stranded coiled coil	8
The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling	8
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	8
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	8
Editorial: Special issue Transporter and Channel	8
Rational peptide design for targeting cancer cell invasion	8
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	8
Assessment of the assessment—All about complexes	8
The avidin‐theophylline complex: A structural and computational study	8
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	8
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	8
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	8
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	8
Issue Information ‐ Table of Content	8
Issue Information ‐ Forthcoming	7
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	7
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp4	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
Transmembrane proteins—Different anchoring systems	7
Prediction of interactions between cell surface proteins by machine learning	7
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	7
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor	7
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	7
The dynamic basis of structural order in proteins	7
Cover Image, Volume 90, Issue 1	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
Issue Information ‐ Table of Content	7
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	7
Low‐frequency collective motion of DNA‐binding domain defines p53 function	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
α/β Hydrolases: Toward Unraveling Entangled Classification	7
Issue Information ‐ Table of Content	7
Structural Classification Insights Into the Plant Defensive Peptides	7
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	6
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Plastic structures for diverse substrates: A revisit of human ABC transporters	6
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Updates to the CASP Infrastructure in 2024	6
Energetic and structural insights behind calcium induced conformational transition in calmodulin	6
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	6
Proteome analysis of the circadian clock protein PERIOD2	6
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
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HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	6
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	6
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	6
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Assessment of three‐dimensional RNA structure prediction in CASP15	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	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
Crystal structure of an L‐type lectin domain from archaea	6
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	6
Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6

Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
ScaffoldMatcher:A CMA‐ESbased algorithm for identifying hotspot aligned peptidomimetic scaffolds	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
What can AlphaFold do for antimicrobial amyloids?	5
Issue Information ‐ Table of Content	5
Exploring Compactness and Dynamics of Apomyoglobin	5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	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 Kinase	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
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Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes	5
Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	5
Cover Image, Volume 91, Issue 12	5
Issue Information ‐ Table of Content	5
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	5
Issue Information ‐ Table of Content	5
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Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	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
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
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 Kinase Structures	4
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	4
Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	4
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
Issue Information ‐ Table of Content	4
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	4
Challenges in bridging the gap between protein structure prediction and functional interpretation	4
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	4
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	4
The following articles for this Special Issue were published in different Issues	4
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	4
SARS‐CoV‐2 main protease mutation analysis via a kinematic method	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
Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation	4
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Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella Typhi	4
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Aspergillus oryzae α‐l‐rhamnosidase: Crystal structure and insight into the substrate specificity	4
Issue Information ‐ Forthcoming	4
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Understanding the Role of RING‐Between‐RING E3 Ligase of the Human Malaria Parasite	4
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies	4
The Crystal Structure of the Domain of Unknown Function 1480 (DUF1480) From Klebsiella pneumoniae	4
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	4
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
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In silico study predicts a key role of RNA‐binding domains 3 and 4 in nucleolin–miRNA interactions	4
Issue Information ‐ Forthcoming	4
Cover Image, Volume 93, Issue 11	4
Protein aggregates thermodynamically order regardless of sequence	4
Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	3
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Issue Information ‐ Table of Content	3
Improving protein structure prediction with extended sequence similarity searches and deep‐learning‐based refinement in CASP15	3
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	3
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	3
New prediction categories in CASP15	3
Conformational Dynamics and Molecular Characterization of Alsin MORN Monomer and Dimeric Assemblies	3
The high identity of the Trypanosoma cruziGroup‐I of trans‐sialidases points them as promising vaccine immunogens	3
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	3
Benchmarking the accuracy of structure‐based binding affinity predictors on Spike–ACE2 deep mutational interaction set	3
In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein–Protein Interactions	3
Protein–Protein Interaction Prediction via Structure‐Based Deep Learning	3
Cover Image, Volume 90, Issue 7	3
Issue Information ‐ Forthcoming	3
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units	3
Structure of the Complex of Lactoperoxidase With Nitric Oxide at 1.95 Å Resolution	3
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	3
The role of leucine and isoleucine in tuning the hydropathy of class A GPCRs	3
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	3
II. Geometrical framework for thinking about globular proteins: The power of poking	3
The human ribosome‐associated complex suppresses prion formation in yeast	3
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Oxidation of active cysteines mediates protein aggregation of S10R, the cataract‐associated mutant of mouse GammaB‐crystallin	3
Structural basis for peptide recognition by archaeal oligopeptide permease A	3
Protein–Ligand Structure Prediction by Template‐Guided Ensemble Docking Strategy	3
Issue Information ‐ Forthcoming	3
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Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	3
Estimation of model accuracy in CASP15 using the ModFOLDdock server	3
Plastics degradation by hydrolytic enzymes: Theplastics‐activeenzymes database—PAZy	3
Structural Basis for the Essential Role of Ca2+ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin‐Resistant Staphylococcus aur	3
Circuit topology predicts pathogenicity of missense mutations	3