Proteins-Structure Function and Bioinformatics

Article	Citations
	145
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	145
Issue Information ‐ Table of Content	117
Protein structuromics: A new method for protein structure–function crosstalk in glioma	87
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	76
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	72
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	63
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	59
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	58
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	51
rrQNet : Protein contact map quality estimation by deep evolutionary reconciliation	50
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	47
Molecular dynamics studies of CED ‐4/ CED ‐9/ EGL	45
Oxygen‐insensitive nitroreductase E. coli NfsA , but not NfsB , is inhi	39
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	39
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	38
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	36
Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding	36
Issue Information ‐ Table of Content	35
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	34
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	32
Crystal structure of GTP ‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	26
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	25
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein	23
Biochemical, Biophysical, and Mechanistic Insights on a Putative Oxidoreductase From Mycobacterium tuberculosis	23

Surveying nonvisual arrestins reveals allosteric interactions between functional sites	22
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	22
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	21
Cover Image, Volume 94, Issue 1	21
Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine	21
In Silico Characterization of Bromo‐ DragonFLY Binding to the 5‐ HT 2A	20
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	19
Issue Information ‐ Table of Content	18
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	18
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	17
Comparative Binding Dynamics of Minibinder 8.6 and HBD3 With TLR3 as Adjuvants for Developing a Pe	17
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	16
Annexin A1, A2, A5, and A6 involvement in human pathologies	16
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Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	14
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	14
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	14
Issue Information ‐ Table of Content	14
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog ( TANGO2 ) Protein Reveals an αββα‐Fold Arrangement	13
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	13
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	13
Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With	13
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	13
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	13
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	13
Mechanistic Insights Into the Inhibition of Dengue Virus NS5 Methyltransferase by Herbacetin	13
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	13
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar	13
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	13
Issue Information ‐ Table of Content	12
Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity	12
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The enigmatic HCN channels: A cellular neurophysiology perspective	12
Issue Information ‐ Table of Content	12
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Protein Target Highlights in CASP16 : Insights From the Structure Providers	11
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	11
Efficient and accurate binding free energy calculation of Aβ 9–40 protofilament propagation	11
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Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	11
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	11
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	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
MPA‐Pred : A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	11
VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	10
Rational peptide design for targeting cancer cell invasion	10
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	10
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	10
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	10

Issue Information ‐ Table of Content	10
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	10
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	10
Tertiary structure assessment at CASP15	10
Issue Information ‐ Table of Content	10
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	10
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	10
Graph_RG: Dominating CASP16 's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	10
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	9
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	9
Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α	9
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	9
Universal and Lineage‐Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms	9
The avidin‐theophylline complex: A structural and computational study	9
Assessment of the assessment—All about complexes	9
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	9
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	9
Cover Image, Volume 93, Issue 12	9
Exploiting protein language models for the precise classification of ion channels and ion transporters	9
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	9
Analysis of the crystal structure of a parallel three‐stranded coiled coil	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
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
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	8
Transmembrane proteins—Different anchoring systems	8
Issue Information ‐ Table of Content	8
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	8
Distinct Substrate and Intermediate Recognition via Mutation Effects on Mycobacterium tuberculosis	8
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	8
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	8
Based on Molecular Docking, Molecular Dynamics Simulation and MM / PB ( G	8
α/β Hydrolases: Toward Unraveling Entangled Classification	8
Issue Information ‐ Table of Content	8
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Editorial: Special issue Transporter and Channel	8
Cross‐linking disulfide bonds govern solution structures of diabodies	8
Structural and Biophysical Characterization of the Yersinia Type Three Secretion System ATPase YscN	8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	8
CRMSNet : A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for	8
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	7
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	7
Issue Information ‐ Table of Content	7
Updates to the CASP Infrastructure in 2024	7
Cover Image, Volume 94, Issue 1	7
Structure and Dynamics of Cannabinoid Binding to the GABA A Receptor	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94  kDa	7
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
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Structural Classification Insights Into the Plant Defensive Peptides	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
Energetic and structural insights behind calcium induced conformational transition in calmodulin	7
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
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Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
Exploring Compactness and Dynamics of Apomyoglobin	6
Atomistic insight into the luminal allosteric regulation of vesicular glutamate transporter 2 by chloride and protons: An all‐atom molecular dynamics simulation study	6
Issue Information ‐ Table of Content	6
Assessment of three‐dimensional RNA structure prediction in CASP15	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
Crystal structure of an L‐type lectin domain from archaea	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	6
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
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Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Dynamical changes of SARS‐CoV ‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
Issue Information ‐ Forthcoming	6
AlphaFold2 ‐Guided Cyclic Peptide Stabilizer Design to Target Protein–Protein Interactions	6
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	6
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP ‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	6

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Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Structural Implications of HIV ‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	5
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	5
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	5
Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella	5
Correction to Structural Classification Insights Into the Plant Defensive Peptides	5
Scaffold Matcher : A CMA‐ES based algorithm for identifying hotspot aligned peptidomimetic scaffol	5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
Aspergillus oryzae α‐ l ‐rhamnosidase: Crystal structure and insigh	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Issue Information ‐ Table of Content	5
Understanding the Role of RING ‐Between‐ RING E3 Ligase of the Human Malaria Parasite	5
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF	5
Issue Information ‐ Table of Content	5
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
Cover Image, Volume 93, Issue 11	5
Interplay of Ser273 Phosphorylation and K268 and K293 Acetylation in PPAR	5
AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold ‐Based K	5
Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	5
Cover Image, Volume 94, Issue 4	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
The Crystal Structure of the Domain of Unknown Function 1480 ( DUF1480 ) From Klebsiella pneumoniae	5
SARS‐CoV ‐2 main protease mutation analysis via a kinematic method	5
Protein aggregates thermodynamically order regardless of sequence	5
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	5
Cover Image, Volume 91, Issue 12	5
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Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
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What can AlphaFold do for antimicrobial amyloids?	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV ‐2 neutralizing antibodies	5
Cyan Thermal Proteins Derived From Thermal Green Protein	4
Issue Information ‐ Table of Content	4
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
DeepUSPS : Deep Learning‐Empowered Unconstrained‐Structural Protein Sequence Design	4
Outer membrane β‐barrel structure prediction through the lens of AlphaFold2	4
A geometrical framework for thinking about proteins	4
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Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	4
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Challenges in bridging the gap between protein structure prediction and functional interpretation	4
Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn (	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	4
Insights Into the Molecular Interactions of MIC2 and M2AP : Role of TSR6<	4
PCANN Program for Structure‐Based Prediction of Protein–Protein Binding Affinity: Comparison With Other Neural‐Network Predictors	4
SARS ‐ CoV ‐2 Mpro Dihedral Angles Reveal Allosteric Signaling	4
Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis	4
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
Role of Extracellular Histidine Residues for the Function and pH Sensitivity of Human Organic Anion Transporting Polypeptide	4
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
Issue Information ‐ Forthcoming	4
Issue Information ‐ Table of Content	4
Issue Information ‐ Table of Content	4
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	4
Secondary structure and toxicity of lysozyme fibrils are determined by the length and unsaturation of phosphatidic acid	4
Cover Image, Volume 90, Issue 11	4
Issue Information ‐ Table of Content	4
Structural Basis for M2 ‐2– MAVS Proteins Interaction in Human Metapneumovirus (	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
Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
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Issue Information ‐ Forthcoming	4
Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
Insight Into Factors Influencing the Aggregation Process in Wild‐Type and P66R Mutant SOD1 : Compu	4
Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition	4
Protein–Protein Interaction Prediction via Structure‐Based Deep Learning	3
Issue Information ‐ Forthcoming	3
Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics	3
AmyloPick : A New Feature Selection Method and Proper Evaluation for Amyloid Hexapeptides and Aggregation‐Prone Regions Prediction	3
DisDock : A Deep Learning Method for Metal Ion‐Protein Redocking	3
Benchmarking the accuracy of structure‐based binding affinity predictors on Spike–ACE2 deep mutational interaction set	3
Biochemical, structural, and kinetic characterization of PPi‐dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii	3
On the Variation of Structural Divergence Among Residues in Enzyme Evolution	3
Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention	3
Shear‐Induced Structural Changes Drive Amorphous Aggregate Formation of Human Insulin	3
Structure and Mechanism of PhdC , a Prenylated‐Flavin Maturase	3
Effects of the Jokela type of spinal muscular atrophy‐related G66V mutation on the structural ensemble characteristics of CHCHD10	3
GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function	3
The Curious Case of CysE : Diversity and Distribution of Serine Acetyltransferases in Bacteria	3
Protein–Ligand Structure Prediction by Template‐Guided Ensemble Docking Strategy	3
Computational Characterization of the Role of LEM2 / LaminA Interactions on the Stability of	3
The impact of AI ‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15	3
In‐silico identification of Tyr232 in AMPKα2 as a dephosphorylation site for the protein tyrosine phosphatase PTP‐PEST	3
Effect of maleylation and denaturation of human serum albumin on its interaction with scavenger receptors	3
Novel Insights Into the Dynamic Conformational Transitions and Active Site Plasticity of Human Immunoregulatory Cathepsin S	3
Interfacial residues in protein–protein complexes are in the eyes of the beholder	3