Proteins-Structure Function and Bioinformatics

Article	Citations
	407
Issue Information ‐ Forthcoming	322
	275
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	154
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	139
Protein structuromics: A new method for protein structure–function crosstalk in glioma	97
Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi	69
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	62
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	56
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods	55
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	55
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	52
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	51
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	49
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	46
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules	45
Entropy‐based distance cutoff for protein internal contact networks	44
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	43
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	42
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	42
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	40
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	38
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	38
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	36
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	36

Surveying nonvisual arrestins reveals allosteric interactions between functional sites	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 benchmark	35
Structure memes: Intuitive visualization of sequence logo and subfamily logo information in a 3D protein‐structural context	33
Issue Information ‐ Forthcoming	32
Issue Information ‐ Table of Content	32
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	30
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	30
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction	29
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	29
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	28
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	27
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides	27
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	26
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	26
Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site‐directed mutagenesis	26
Annexin A1, A2, A5, and A6 involvement in human pathologies	25
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity	24
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	23
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	22
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	22
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	21
The denatured state of HIV‐1 protease under native conditions	21
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	20
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	20
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	20
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	20
	20
Issue Information ‐ Table of Content	19
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	19
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	19
	19
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	19
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	18
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	17
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches	17
The enigmatic HCN channels: A cellular neurophysiology perspective	17
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	17
	16
Issue Information ‐ Table of Content	16
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	16
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design	15
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	15
Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation	15
Evidence for the preferential reuse of sub‐domain motifs in primordial protein folds	15
	14
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	14
Issue Information ‐ Table of Content	14
Issue Information ‐ Table of Content	14
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments	14
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	13

The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	13
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses	12
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP	12
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	12
	12
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	12
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles	11
Biological nanopores for sensing applications	11
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	11
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	11
Tertiary structure assessment at CASP15	10
	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
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	10
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	10
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	10
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	10
A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes	9
Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations	9
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	9
Analysis of the crystal structure of a parallel three‐stranded coiled coil	9
The avidin‐theophylline complex: A structural and computational study	9
Issue Information ‐ Table of Content	9
The amyloid concentric β‐barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels	9
Issue Information ‐ Table of Content	9
Rational peptide design for targeting cancer cell invasion	9
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	8
Exploiting protein language models for the precise classification of ion channels and ion transporters	8
Transmembrane proteins—Different anchoring systems	8
The dynamic basis of structural order in proteins	8
Assessing the accuracy of contact and distance predictions in CASP14	8
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	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
Issue Information ‐ Table of Content	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
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	8
Assessment of the assessment—All about complexes	8
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	8
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	8
α/β Hydrolases: Toward Unraveling Entangled Classification	8
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	8
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
Editorial: Special issue Transporter and Channel	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Assessing the binding properties of CASP14 targets and models	7
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	7
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	7
Cross‐linking disulfide bonds govern solution structures of diabodies	7
The functional motions and related key residues behind the uncoating of coxsackievirus A16	7
The role of lysine acetylation in the function of mitochondrial ribosomal protein L12	7
Prediction of interactions between cell surface proteins by machine learning	7
Cover Image, Volume 90, Issue 1	7
Issue Information ‐ Table of Content	7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	7
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	7
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp4	7
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	7
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Issue Information ‐ Forthcoming	7
Crystal structure of an L‐type lectin domain from archaea	6
Iterated local search with partition crossover for computational protein design	6
Cover Image, Volume 89, Issue 11	6
Energetic and structural insights behind calcium induced conformational transition in calmodulin	6
	6
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	6
Scoring of protein–protein docking models utilizing predicted interface residues	6
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	6
Plastic structures for diverse substrates: A revisit of human ABC transporters	6
Issue Information ‐ Forthcoming	6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	6
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	6

TetR and OmpR family regulators in natural product biosynthesis and resistance	6
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	6
Proteome analysis of the circadian clock protein PERIOD2	6
High‐accuracy protein structure prediction in CASP14	6
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	6
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	6
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor	6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	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
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
	6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	6
Issue Information ‐ Table of Content	6
	6
Cover Image, Volume 89, Issue 9	6
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	6
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	6
Issue Information ‐ Forthcoming	6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	6
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	6
The following articles for this Special Issue were published in different Issues	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	5
	5
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	5
Issue Information ‐ Forthcoming	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies	5
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks	5
Cover Image, Volume 89, Issue 9	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
Interplay between hydrogen and chalcogen bonds in cysteine	5
Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes	5
	5
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	5
Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	5
	5
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	5
Issue Information ‐ Table of Content	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Exploring Compactness and Dynamics of Apomyoglobin	5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	5
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	5
What can AlphaFold do for antimicrobial amyloids?	5
Issue Information ‐ Table of Content	5
Assessment of three‐dimensional RNA structure prediction in CASP15	5
	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
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5