Proteins-Structure Function and Bioinformatics

Article	Citations
	415
Issue Information ‐ Forthcoming	332
	278
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	159
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	146
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations	100
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	72
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching	68
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules	56
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	55
Entropy‐based distance cutoff for protein internal contact networks	55
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods	54
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	53
Protein structuromics: A new method for protein structure–function crosstalk in glioma	52
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	51
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	44
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	44
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
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	38
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	38
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	36

Issue Information ‐ Forthcoming	36
Issue Information ‐ Table of Content	36
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	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	33
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	33
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	31
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	30
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides	30
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	29
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	29
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	29
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes	26
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics	26
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity	26
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism	25
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature	25
Annexin A1, A2, A5, and A6 involvement in human pathologies	24
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation	24
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	23
The denatured state of HIV‐1 protease under native conditions	23
Issue Information ‐ Table of Content	22
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	22
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus	22
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	22
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	21
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Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity	20
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity	20
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme	20
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides	19
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation	19
The enigmatic HCN channels: A cellular neurophysiology perspective	19
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches	18
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Issue Information ‐ Table of Content	17
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CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	16
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server	16
Issue Information ‐ Table of Content	16
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes	15
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX4	15
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix	14
Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation	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
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein	14
Biological nanopores for sensing applications	13
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom	12

Tertiary structure assessment at CASP15	12
The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes	12
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles	12
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	12
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments	12
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	12
Issue Information ‐ Table of Content	11
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome	11
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding	11
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	11
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily	11
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Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein	11
Atomistic molecular simulations of Aβ‐Zn conformational ensembles	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
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)	10
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	10
Analysis of the crystal structure of a parallel three‐stranded coiled coil	10
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase	10
The avidin‐theophylline complex: A structural and computational study	10
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor	9
Issue Information ‐ Table of Content	9
A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes	9
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	9
Rational peptide design for targeting cancer cell invasion	9
Assessment of the assessment—All about complexes	9
The amyloid concentric β‐barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels	9
Exploiting protein language models for the precise classification of ion channels and ion transporters	9
α/β Hydrolases: Toward Unraveling Entangled Classification	9
Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations	9
The dynamic basis of structural order in proteins	8
Editorial: Special issue Transporter and Channel	8
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp4	8
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference	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
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	8
Prediction of interactions between cell surface proteins by machine learning	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
Transmembrane proteins—Different anchoring systems	8
Cover Image, Volume 90, Issue 1	8
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	8
Low‐frequency collective motion of DNA‐binding domain defines p53 function	8
Assessing the accuracy of contact and distance predictions in CASP14	8
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi	8
The functional motions and related key residues behind the uncoating of coxsackievirus A16	8
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi	8
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	8
Issue Information ‐ Forthcoming	8
Cross‐linking disulfide bonds govern solution structures of diabodies	8
Cover Image, Volume 89, Issue 9	7
TetR and OmpR family regulators in natural product biosynthesis and resistance	7
Scoring of protein–protein docking models utilizing predicted interface residues	7
Assessing the binding properties of CASP14 targets and models	7
Issue Information ‐ Table of Content	7
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	7
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	7
Energetic and structural insights behind calcium induced conformational transition in calmodulin	7
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	7
Cover Image, Volume 89, Issue 11	7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	7
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor	7
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
Issue Information ‐ Table of Content	7
Plastic structures for diverse substrates: A revisit of human ABC transporters	7
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Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	7
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis	7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	7
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	7
High‐accuracy protein structure prediction in CASP14	7
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein	6
Exploring Compactness and Dynamics of Apomyoglobin	6

Issue Information ‐ Forthcoming	6
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On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	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
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
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	6
Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes	6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein	6
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease	6
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Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	6
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Iterated local search with partition crossover for computational protein design	6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	6
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	6
Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	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
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers	6
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The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants	6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	6
Crystal structure of an L‐type lectin domain from archaea	6
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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
Assessment of three‐dimensional RNA structure prediction in CASP15	6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	6
What can AlphaFold do for antimicrobial amyloids?	6
Interplay between hydrogen and chalcogen bonds in cysteine	5
ScaffoldMatcher:A CMA‐ESbased algorithm for identifying hotspot aligned peptidomimetic scaffolds	5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies	5
Predicting mutant outcome by combining deep mutational scanning and machine learning	5
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis	5
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase	5
Structural Implications of HIV‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study	5
Cover Image, Volume 89, Issue 7	5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	5
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods	5
Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies	5
High‐Throughput Evaluation of Natural Diversity of F‐Type ATP Synthase Rotor Ring Stoichiometries	5
Understanding the Role of RING‐Between‐RING E3 Ligase of the Human Malaria Parasite	5
The Crystal Structure of the Domain of Unknown Function 1480 (DUF1480) From Klebsiella pneumoniae	5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	5
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	5
Issue Information ‐ Table of Content	5
Protein model quality assessment using rotation‐equivariant transformations on point clouds	5
Cover Image, Volume 89, Issue 9	5
The following articles for this Special Issue were published in different Issues	5
Protein aggregates thermodynamically order regardless of sequence	5
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Investigating Local Sequence‐Structural Attributes of Amyloidogenic Light Chain Variable Domains	5
Cover Image, Volume 91, Issue 12	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
Cover Image, Volume 89, Issue 7	5
Issue Information ‐ Table of Content	5
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Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome	4
Physicochemical Evaluation of Remote Homology in the Twilight Zone	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
AbDPP: Target‐oriented antibody design with pretraining and prior biological structure knowledge	4
Functional antibody characterization via direct structural analysis and information‐driven protein–protein docking	4
Issue Information ‐ Forthcoming	4
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory	4
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	4
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors	4
Aspergillus oryzae α‐l‐rhamnosidase: Crystal structure and insight into the substrate specificity	4
Dynamics of binding interactions of TDP‐43 and RNA: An equally weighted multiscale elastic network model study	4
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction	4
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	4
Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies	4
Plastics degradation by hydrolytic enzymes: Theplastics‐activeenzymes database—PAZy	4
Lipid exchange in crystal‐confined fatty acid binding proteins: X‐ray evidence and molecular dynamics explanation	4
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Assessment of the CASP14 assembly predictions	4
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	4
ANOVA‐particle swarm optimization‐based feature selection and gradient boosting machine classifier for improved protein–protein interaction prediction	4
In silico study predicts a key role of RNA‐binding domains 3 and 4 in nucleolin–miRNA interactions	4
SARS‐CoV‐2 main protease mutation analysis via a kinematic method	4
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Outer membrane β‐barrel structure prediction through the lens ofAlphaFold2	4
Insight Into Factors Influencing the Aggregation Process in Wild‐Type and P66R Mutant SOD1: Computational and Spectroscopic Approaches	4
PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation	4
Key substrate recognition residues in the active site of cystathionine beta‐synthase from Toxoplasma gondii	4
Improving the quality of co‐evolution intermolecular contact prediction with DisVis	4
Issue Information ‐ Forthcoming	4
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium	4
Protein oligomer modeling guided by predicted interchain contacts in CASP14	4
In‐silico screening and microsecond molecular dynamics simulations to identify single point mutations that destabilize β‐hexosaminidase A causing Tay‐Sachs disease	4
Challenges in bridging the gap between protein structure prediction and functional interpretation	4