Proteins-Structure Function and Bioinformatics

Article	Citations
	421
Issue Information ‐ Forthcoming	338
	283
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	162
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	154
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	102
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	79
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	78
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	57
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	57
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	55
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules	55
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	54
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods	53
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	52
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	52
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	48
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	45
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	44
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	43
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	42
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	41
Protein structuromics: A new method for protein structure–function crosstalk in glioma	39
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	38
Issue Information ‐ Forthcoming	37

Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	37
Issue Information ‐ Table of Content	37
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	36
Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site‐directed mutagenesis	33
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	33
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	32
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	31
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides	31
Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions	30
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	29
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	29
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	27
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	27
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity	26
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	26
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	25
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	25
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	25
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	24
The denatured state of HIV‐1 protease under native conditions	24
Issue Information ‐ Table of Content	22
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	22
Improving AlphaFold2‐ and AlphaFold3‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP16	22
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	22
Annexin A1, A2, A5, and A6 involvement in human pathologies	21
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	21
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	20
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	20
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Issue Information ‐ Table of Content	20
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	19
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	19
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	19
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	18
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	18
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	18
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches	17
Issue Information ‐ Table of Content	16
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Issue Information ‐ Table of Content	16
The enigmatic HCN channels: A cellular neurophysiology perspective	16
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Issue Information ‐ Table of Content	15
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	14
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	14
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Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	14
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	13
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	13
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments	12

The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	12
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	12
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	12
Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation	12
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	12
Graph_RG: Dominating CASP16's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	11
Tertiary structure assessment at CASP15	11
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	11
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	11
Biological nanopores for sensing applications	11
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	11
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	11
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	11
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	10
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	10
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	10
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	10
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles	10
Issue Information ‐ Table of Content	10
Analysis of the crystal structure of a parallel three‐stranded coiled coil	10
The amyloid concentric β‐barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels	10
Issue Information ‐ Table of Content	10
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	10
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	10
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	10
Assessment of the assessment—All about complexes	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
The avidin‐theophylline complex: A structural and computational study	9
Rational peptide design for targeting cancer cell invasion	9
α/β Hydrolases: Toward Unraveling Entangled Classification	9
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	9
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	9
Exploiting protein language models for the precise classification of ion channels and ion transporters	9
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	9
The dynamic basis of structural order in proteins	8
Editorial: Special issue Transporter and Channel	8
Prediction of interactions between cell surface proteins by machine learning	8
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	8
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	8
Cover Image, Volume 90, Issue 1	8
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	8
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	8
Cross‐linking disulfide bonds govern solution structures of diabodies	8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	8
Transmembrane proteins—Different anchoring systems	8
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	8
Issue Information ‐ Forthcoming	8
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	8
Low‐frequency collective motion of DNA‐binding domain defines p53 function	8
Assessing the accuracy of contact and distance predictions in CASP14	8
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp4	8
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	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
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	8
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	8
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
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Issue Information ‐ Table of Content	7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Energetic and structural insights behind calcium induced conformational transition in calmodulin	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	7
Cover Image, Volume 89, Issue 9	7
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis	7
Issue Information ‐ Table of Content	7
Issue Information ‐ Forthcoming	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
High‐accuracy protein structure prediction in CASP14	7
Cover Image, Volume 89, Issue 11	7
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	7
Assessing the binding properties of CASP14 targets and models	7
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor	7
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	7

CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	7
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
Exploring Compactness and Dynamics of Apomyoglobin	6
New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study	6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	6
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Issue Information ‐ Table of Content	6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	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
Protein model quality assessment using rotation‐equivariant transformations on point clouds	6
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	6
Crystal structure of an L‐type lectin domain from archaea	6
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Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	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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Assessment of three‐dimensional RNA structure prediction in CASP15	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
Iterated local search with partition crossover for computational protein design	6
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	6
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
Issue Information ‐ Forthcoming	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
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On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	6
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Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes	6
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Issue Information ‐ Table of Content	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	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
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
ScaffoldMatcher:A CMA‐ESbased algorithm for identifying hotspot aligned peptidomimetic scaffolds	5
Predicting mutant outcome by combining deep mutational scanning and machine learning	5
Structural Implications of HIV‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
The following articles for this Special Issue were published in different Issues	5
Cover Image, Volume 89, Issue 9	5
Interplay between hydrogen and chalcogen bonds in cysteine	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
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase	5
Issue Information ‐ Table of Content	5
What can AlphaFold do for antimicrobial amyloids?	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies	5
The Crystal Structure of the Domain of Unknown Function 1480 (DUF1480) From Klebsiella pneumoniae	5
Understanding the Role of RING‐Between‐RING E3 Ligase of the Human Malaria Parasite	5
Protein aggregates thermodynamically order regardless of sequence	5