Proteins-Structure Function and Bioinformatics

Article	Citations
	157
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	152
Issue Information ‐ Table of Content	127
Protein structuromics: A new method for protein structure–function crosstalk in glioma	88
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	80
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	76
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	65
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	61
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	60
Molecular dynamics studies of CED ‐4/ CED ‐9/ EGL	56
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	51
Oxygen‐insensitive nitroreductase E. coli NfsA , but not NfsB , is inhi	48
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	46
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	44
Molecular Dynamics Identify Variances Between Galectin Carbohydrate‐Binding Sites That Impact the Binding Site Conformation and Ligand Binding	41
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	40
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	40
Issue Information ‐ Table of Content	37
Crystal structure of GTP ‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	35
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	35
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	33
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein	30
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	28
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	28
Cover Image, Volume 94, Issue 1	26

Biochemical, Biophysical, and Mechanistic Insights on a Putative Oxidoreductase From Mycobacterium tuberculosis	24
In Silico Characterization of Bromo‐ DragonFLY Binding to the 5‐ HT 2A	24
Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine	23
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	22
Structural and Functional Roles of Arg85‐Mediated Inter‐Motif Interactions in Human dUTPase	21
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16	21
Issue Information ‐ Table of Content	20
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	19
Differences in the Activities of Domain‐Swapped Chimeras of Two Homologous GH57 Glucanotransferases Suggest That a Glucan‐Binding	19
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	19
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Issue Information ‐ Table of Content	18
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation	17
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	17
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	16
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	16
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	16
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	16
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar	16
Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With	15
Mechanistic Insights Into the Inhibition of Dengue Virus NS5 Methyltransferase by Herbacetin	15
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	14
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	14
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	14
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	14
Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity	14
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	14
Comparative Binding Dynamics of Minibinder 8.6 and HBD3 With TLR3 as Adjuvants for Developing a Pe	14
The Crystal Structure of Human Transport and Golgi Organization 2 Homolog ( TANGO2 ) Protein Reveals an αββα‐Fold Arrangement	14
The enigmatic HCN channels: A cellular neurophysiology perspective	14
Issue Information ‐ Table of Content	13
Annexin A1, A2, A5, and A6 involvement in human pathologies	13
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis	13
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Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	12
Protein Target Highlights in CASP16 : Insights From the Structure Providers	12
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	12
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	12
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	12
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	12
MPA‐Pred : A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	12
Rational peptide design for targeting cancer cell invasion	11
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	11
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	11
Issue Information ‐ Table of Content	11
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction	11
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium	11
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis	11

Issue Information ‐ Table of Content	11
Tertiary structure assessment at CASP15	11
Efficient and accurate binding free energy calculation of Aβ 9–40 protofilament propagation	11
Graph_RG: Dominating CASP16 's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening	11
VoroIF‐GNN : Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	11
Universal and Lineage‐Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms	10
Analysis of the crystal structure of a parallel three‐stranded coiled coil	10
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	10
The avidin‐theophylline complex: A structural and computational study	10
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	10
The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling	10
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	10
Cover Image, Volume 93, Issue 12	10
Exploiting protein language models for the precise classification of ion channels and ion transporters	10
Generalizing the Gaussian Network Model: Spanning‐Tree Thermodynamics Shows Entropy‐Driven KRAS Activation	10
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	10
Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods	10
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	10
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	10
Assessment of the assessment—All about complexes	9
Distinct Substrate and Intermediate Recognition via Mutation Effects on Mycobacterium tuberculosis	9
Structural and Biophysical Characterization of the Yersinia Type Three Secretion System ATPase YscN	9
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	9
Cross‐linking disulfide bonds govern solution structures of diabodies	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
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	9
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Editorial: Special issue Transporter and Channel	9
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	9
Based on Molecular Docking, Molecular Dynamics Simulation and MM / PB ( G	9
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	9
Prediction of interactions between cell surface proteins by machine learning	9
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	9
Transmembrane proteins—Different anchoring systems	8
CRMSNet : A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for	8
Updates to the CASP Infrastructure in 2024	8
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors	8
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	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
Issue Information ‐ Table of Content	8
Energetic and structural insights behind calcium induced conformational transition in calmodulin	8
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	8
α/β Hydrolases: Toward Unraveling Entangled Classification	8
Issue Information ‐ Table of Content	8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	8
Cover Image, Volume 94, Issue 1	8
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold	8
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	7
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TetR and OmpR family regulators in natural product biosynthesis and resistance	7
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes	7
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
Structure and Dynamics of Cannabinoid Binding to the GABA A Receptor	7
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations	7
Structural Variability of Pfam Domains Based on Alphafold2 Predictions	7
Dynamical changes of SARS‐CoV ‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	7
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94  kDa	7
Crystal structure of an L‐type lectin domain from archaea	7
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	7
Markovian Timescales of Intramolecular Disulfide Pairing in Cyclotides	7
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Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design	6
Assessment of three‐dimensional RNA structure prediction in CASP15	6
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP ‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp90	6
Issue Information ‐ Table of Content	6
Scaffold Matcher : A CMA‐ES based algorithm for identifying hotspot aligned peptidomimetic scaffol	6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	6
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Responses to Ligand Binding in the Bacterial DNA Sliding Clamp “β‐Clamp” Manifest in Dynamic Allosteric Effects	6
Interplay between hydrogen and chalcogen bonds in cysteine	6
Cover Image, Volume 94, Issue 4	6
Comparative Analysis of Deep Learning‐Based Algorithms for Peptide Structure Prediction	6
Protein model quality assessment using rotation‐equivariant transformations on point clouds	6

Issue Information ‐ Table of Content	6
AlphaFold2 ‐Guided Cyclic Peptide Stabilizer Design to Target Protein–Protein Interactions	6
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	6
What can AlphaFold do for antimicrobial amyloids?	6
Interplay of Ser273 Phosphorylation and K268 and K293 Acetylation in PPAR	6
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	6
Exploring Compactness and Dynamics of Apomyoglobin	6
Understanding the Role of RING ‐Between‐ RING E3 Ligase of the Human Malaria Parasite	5
Issue Information ‐ Forthcoming	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
Correction to Structural Classification Insights Into the Plant Defensive Peptides	5
Cover Image, Volume 91, Issue 12	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
Cover Image, Volume 93, Issue 11	5
Issue Information ‐ Table of Content	5
Structural and Comparative Stability of a Truncated N‐Terminal Domain of DNA Gyrase A From Salmonella	5
Issue Information ‐ Table of Content	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV ‐2 neutralizing antibodies	5
Issue Information ‐ Forthcoming	5
Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Aspergillus oryzae α‐ l ‐rhamnosidase: Crystal structure and insigh	5
Issue Information ‐ Table of Content	5
Protein aggregates thermodynamically order regardless of sequence	5
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AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold ‐Based K	5
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Structural Implications of HIV ‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	5
Challenges in bridging the gap between protein structure prediction and functional interpretation	5
Physics‐Based Energy Functions for Computational Protein Design	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF	5
Structural and Stability Analysis of de Novo Designed Proteins Incorporating a Plant Self‐Incompatibility Motif	5
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A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	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
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