Proteins-Structure Function and Bioinformatics

Article	Citations
	201
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	142
Issue Information ‐ Table of Content	140
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	112
Protein structuromics: A new method for protein structure–function crosstalk in glioma	86
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	76
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	70
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	63
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	58
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	58
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	51
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	50
rrQNet : Protein contact map quality estimation by deep evolutionary reconciliation	46
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	44
Molecular dynamics studies of CED ‐4/ CED ‐9/ EGL	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	38
Oxygen‐insensitive nitroreductase E. coli NfsA , but not NfsB , is inhi	37
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	35
Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding	34
Issue Information ‐ Table of Content	34
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	32
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	31
Cover Image, Volume 94, Issue 1	26
In Silico Characterization of Bromo‐ DragonFLY Binding to the 5‐ HT 2A	24
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	23

An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein	22
Crystal structure of GTP ‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	22
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	22
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	21
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	20
Biochemical, Biophysical, and Mechanistic Insights on a Putative Oxidoreductase From Mycobacterium tuberculosis	19
Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine	19
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	18
Issue Information ‐ Table of Content	17
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	17
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	17
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	16
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	16
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog ( TANGO2 ) Protein Reveals an αββα‐Fold Arrangement	15
Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity	14
Issue Information ‐ Table of Content	13
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	13
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	13
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Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	13
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	13
Mechanistic Insights Into the Inhibition of Dengue Virus NS5 Methyltransferase by Herbacetin	13
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	13
Comparative Binding Dynamics of Minibinder 8.6 and HBD3 With TLR3 as Adjuvants for Developing a Pe	13
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar	12
The enigmatic HCN channels: A cellular neurophysiology perspective	12
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	12
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	12
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	12
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	12
Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With	12
Protein Target Highlights in CASP16 : Insights From the Structure Providers	11
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Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	11
Tertiary structure assessment at CASP15	11
Issue Information ‐ Table of Content	11
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Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	11
Issue Information ‐ Table of Content	11
Annexin A1, A2, A5, and A6 involvement in human pathologies	11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	10
MPA‐Pred : A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	10
VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	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
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	10
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	10
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	10
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	10

Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	10
Graph_RG: Dominating CASP16 's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	10
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	10
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	9
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	9
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	9
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	9
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	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
Issue Information ‐ Table of Content	9
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	9
The avidin‐theophylline complex: A structural and computational study	9
Issue Information ‐ Table of Content	9
Cover Image, Volume 93, Issue 12	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
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	9
Rational peptide design for targeting cancer cell invasion	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
Analysis of the crystal structure of a parallel three‐stranded coiled coil	9
Assessment of the assessment—All about complexes	9
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	9
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Transmembrane proteins—Different anchoring systems	8
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	8
Issue Information ‐ Table of Content	8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	8
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	8
Prediction of interactions between cell surface proteins by machine learning	8
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	8
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	8
α/β Hydrolases: Toward Unraveling Entangled Classification	8
Editorial: Special issue Transporter and Channel	8
Structural and Biophysical Characterization of the Yersinia Type Three Secretion System ATPase YscN	8
Cross‐linking disulfide bonds govern solution structures of diabodies	8
Based on Molecular Docking, Molecular Dynamics Simulation and MM / PB ( G	8
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	8
Distinct Substrate and Intermediate Recognition via Mutation Effects on Mycobacterium tuberculosis	8
Issue Information ‐ Table of Content	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Crystal structure of an L‐type lectin domain from archaea	7
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94  kDa	7
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	7
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
CRMSNet : A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for	7
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	7
Issue Information ‐ Forthcoming	7
Updates to the CASP Infrastructure in 2024	7
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Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
Cover Image, Volume 94, Issue 1	7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
Energetic and structural insights behind calcium induced conformational transition in calmodulin	7
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Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Structure and Dynamics of Cannabinoid Binding to the GABA A Receptor	7
Issue Information ‐ Table of Content	7
Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
AlphaFold2 ‐Guided Cyclic Peptide Stabilizer Design to Target Protein–Protein Interactions	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
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Interplay between hydrogen and chalcogen bonds in cysteine	6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	6
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	6
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	6
Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	6
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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
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	6
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	6
Assessment of three‐dimensional RNA structure prediction in CASP15	6
Issue Information ‐ Table of Content	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
TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Issue Information ‐ Table of Content	5
The Crystal Structure of the Domain of Unknown Function 1480 ( DUF1480 ) From Klebsiella pneumoniae	5
Cover Image, Volume 94, Issue 4	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
Protein aggregates thermodynamically order regardless of sequence	5
Understanding the Role of RING ‐Between‐ RING E3 Ligase of the Human Malaria Parasite	5
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	5
Cover Image, Volume 93, Issue 11	5
Issue Information ‐ Table of Content	5
Protein folding and unfolding: proline cis ‐ trans isomerization at the c	5
The following articles for this Special Issue were published in different Issues	5
AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold ‐Based K	5
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	5
Interplay of Ser273 Phosphorylation and K268 and K293 Acetylation in PPAR	5
Exploring Compactness and Dynamics of Apomyoglobin	5
What can AlphaFold do for antimicrobial amyloids?	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV ‐2 neutralizing antibodies	5
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Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	5
IGPRED : Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
Cover Image, Volume 91, Issue 12	5
Structural Implications of HIV ‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP ‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF	5
SARS‐CoV ‐2 main protease mutation analysis via a kinematic method	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
Scaffold Matcher : A CMA‐ES based algorithm for identifying hotspot aligned peptidomimetic scaffol	5
Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella	5
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The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
Correction to Structural Classification Insights Into the Plant Defensive Peptides	4
In silico study predicts a key role of RNA ‐binding domains 3 and 4 in nucleolin–miRNA interaction	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
PCNA from Thermococcus gammatolerans : A protein involved in chromosomal DNA metabolism intrinsically	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	4
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	4
Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn (	4
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Structural Basis for M2 ‐2– MAVS Proteins Interaction in Human Metapneumovirus (	4
Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
Conformational Dynamics and Molecular Characterization of Alsin MORN Monomer and Dimeric Assemblies	4
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Issue Information ‐ Forthcoming	4
Aspergillus oryzae α‐ l ‐rhamnosidase: Crystal structure and insigh	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	4
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AlphaFold and Docking Approaches for Antibody–Antigen and Other Targets: Insights From CAPRI Rounds 47–55	4
Insight Into Factors Influencing the Aggregation Process in Wild‐Type and P66R Mutant SOD1 : Compu	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
DeepUSPS : Deep Learning‐Empowered Unconstrained‐Structural Protein Sequence Design	4
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies	4
Issue Information ‐ Table of Content	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
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A geometrical framework for thinking about proteins	4
Issue Information ‐ Table of Content	4
Outer membrane β‐barrel structure prediction through the lens of AlphaFold2	4
Issue Information ‐ Table of Content	4
Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
Role of Extracellular Histidine Residues for the Function and pH Sensitivity of Human Organic Anion Transporting Polypeptide	4
Issue Information ‐ Forthcoming	4
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	4
Novel Insights Into the Dynamic Conformational Transitions and Active Site Plasticity of Human Immunoregulatory Cathepsin S	3
Issue Information ‐ Forthcoming	3
Biochemical, structural, and kinetic characterization of PPi‐dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii	3
The Curious Case of CysE : Diversity and Distribution of Serine Acetyltransferases in Bacteria	3
Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in	3
In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein–Protein Interactions	3
Benchmarking the accuracy of structure‐based binding affinity predictors on Spike–ACE2 deep mutational interaction set	3
The human ribosome‐associated complex suppresses prion formation in yeast	3
Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention	3
The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation	3
AmyloPick : A New Feature Selection Method and Proper Evaluation for Amyloid Hexapeptides and Aggregation‐Prone Regions Prediction	3
Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	3
Interfacial residues in protein–protein complexes are in the eyes of the beholder	3
Protein Involved in Initiation 1 Interaction With Starch Synthase 4 From Arabidopsis thaliana Induces Inhibition of Elongating Activity	3
Computational Characterization of the Role of LEM2 / LaminA Interactions on the Stability of	3
Structure and Mechanism of PhdC , a Prenylated‐Flavin Maturase	3
Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated resi	3
Protein–Ligand Structure Prediction by Template‐Guided Ensemble Docking Strategy	3
On the Variation of Structural Divergence Among Residues in Enzyme Evolution	3
Protein–Protein Interaction Prediction via Structure‐Based Deep Learning	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
Massive Sampling Strategy for Antibody–Antigen Targets in CAPRI Round 55 With MassiveFold	3
Crystal structure of the catalytic ATP ‐binding domain of the PhoR sensor histidine kinase	3