Proteins-Structure Function and Bioinformatics

Papers
(The TQCC of Proteins-Structure Function and Bioinformatics is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-07-01 to 2025-07-01.)
ArticleCitations
421
Issue Information ‐ Forthcoming338
283
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network162
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus154
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations102
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching79
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 78
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate57
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases57
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment55
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules55
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor54
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods53
SARS‐CoV‐2 neutralizing antibody epitopes are overlapping and highly mutated which raises the chances of escape variants and requires development of broadly reactive vaccines52
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective52
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.048
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation45
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation44
New simulation insights on the structural transition mechanism of bovine rhodopsin activation43
Molecular dynamics studies of CED‐4/CED‐9/EGL‐1 ternary complex reveal CED‐4 release mechanism in the linear apoptotic pathway of Caenorhabditis ele42
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins41
Protein structuromics: A new method for protein structure–function crosstalk in glioma39
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain38
Issue Information ‐ Forthcoming37
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis37
Issue Information ‐ Table of Content37
An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction36
Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site‐directed mutagenesis33
Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x‐ray reference structures as a prediction benchmark33
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF32
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides31
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides31
Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions30
Surveying nonvisual arrestins reveals allosteric interactions between functional sites29
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction29
Location of S‐nitrosylated cysteines in protein three‐dimensional structures27
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data27
Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity26
A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics26
PredictingDNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature25
A Novel Tetravalent CD95/Fas Fusion Protein With Superior CD95L/FasL Antagonism25
Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation25
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing24
The denatured state of HIV‐1 protease under native conditions24
Issue Information ‐ Table of Content22
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches22
Improving AlphaFold2‐ and AlphaFold3‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP1622
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc4222
Annexin A1, A2, A5, and A6 involvement in human pathologies21
Exploring the Effect of Hydrocarbon Cross‐Linkers on the Structure and Binding of Stapled p53 Peptides21
Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)‐Ib From Campylobacter fetus subsp. fetus20
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP1520
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Issue Information ‐ Table of Content20
Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme19
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity19
Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity19
Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes18
Allium sativum‐Derived Alliin and Allicin Stably Bind to α‐Synuclein and Prevent Its Cytotoxic Aggregation18
Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation18
Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches17
Issue Information ‐ Table of Content16
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Issue Information ‐ Table of Content16
The enigmatic HCN channels: A cellular neurophysiology perspective16
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Issue Information ‐ Table of Content15
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps14
A Closer Look at Type I Left‐Handed β‐Helices Provides a Better Understanding in Their Sequence–Structure Relationship: Toward Their Rational Design14
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Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server14
Dynamics and recognition of homeodomain containing protein‐DNA complex of IRX413
MPA‐Pred: A machine learning approach for predicting the binding affinity of membrane protein–protein complexes13
The C‐terminal extension of VgrG4 from Klebsiella pneumoniae remodels host cell microfilaments12
The non‐prion SUP35 preexists in large chaperone‐containing molecular complexes12
Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein12
Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein12
Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation12
Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom12
Graph_RG: Dominating CASP16's Small Molecule Affinity Prediction Subcategory—A Pose‐Free Framework for Billion‐Scale Virtual Screening11
Tertiary structure assessment at CASP1511
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network11
Structural and Functional Analysis of Plant Oil‐Body Lipase EgLIP1 From Elaeis guineensis11
Biological nanopores for sensing applications11
In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis11
The High‐Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix11
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins11
Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium11
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐1910
AlphaFold2‐guided description ofCoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily10
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome10
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins10
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles10
Issue Information ‐ Table of Content10
Analysis of the crystal structure of a parallel three‐stranded coiled coil10
The amyloid concentric β‐barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels10
Issue Information ‐ Table of Content10
Structural Basis for Monomer–Dimer Transition of Dri1 Upon Heme Binding10
Atomistic molecular simulations of Aβ‐Zn conformational ensembles10
An intrinsic network of polar interactions is responsible for binding of UL49.5 C‐degron by the CRL2KLHDC3 ubiquitin ligase10
Assessment of the assessment—All about complexes9
The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling9
The avidin‐theophylline complex: A structural and computational study9
Rational peptide design for targeting cancer cell invasion9
α/β Hydrolases: Toward Unraveling Entangled Classification9
Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)9
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor9
Exploiting protein language models for the precise classification of ion channels and ion transporters9
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)9
The dynamic basis of structural order in proteins8
Editorial: Special issue Transporter and Channel8
Prediction of interactions between cell surface proteins by machine learning8
Improved NMR‐data‐compliant protein structure modeling captures context‐dependent variations and expands the scope of functional inference8
The role of lysine acetylation in the function of mitochondrial ribosomal protein L128
Cover Image, Volume 90, Issue 18
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol8
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins8
Cross‐linking disulfide bonds govern solution structures of diabodies8
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms8
Transmembrane proteins—Different anchoring systems8
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors8
Issue Information ‐ Forthcoming8
Structure of a transmission blocking antibody in complex with Outer surface protein A from the Lyme disease spirochete, Borreliella burgdorferi8
Low‐frequency collective motion of DNA‐binding domain defines p53 function8
Assessing the accuracy of contact and distance predictions in CASP148
Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV‐Nsp48
Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi8
Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α8
Prediction of protein–protein interactions using sequences of intrinsically disordered regions8
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function8
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes7
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Issue Information ‐ Table of Content7
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 27
Scoring of protein–protein docking models utilizing predicted interface residues7
Plastic structures for diverse substrates: A revisit of human ABC transporters7
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold7
Energetic and structural insights behind calcium induced conformational transition in calmodulin7
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP27
Investigating the Context‐Dependent Phase Separation of Human HOX Transcription Factors7
Cover Image, Volume 89, Issue 97
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods7
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)7
Structural Classification Insights Into the Plant Defensive Peptides7
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis7
Issue Information ‐ Table of Content7
Issue Information ‐ Forthcoming7
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species7
High‐accuracy protein structure prediction in CASP147
Cover Image, Volume 89, Issue 117
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP147
Assessing the binding properties of CASP14 targets and models7
Structure and Dynamics of Cannabinoid Binding to the GABAA Receptor7
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor7
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence7
Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design6
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective6
Exploring Compactness and Dynamics of Apomyoglobin6
New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study6
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions6
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein6
CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces6
Issue Information ‐ Table of Content6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands6
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro6
Proteome analysis of the circadian clock protein PERIOD26
Protein model quality assessment using rotation‐equivariant transformations on point clouds6
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images6
Hereditary Amyloidosis: Insights Into a Fibrinogen A Variant Protein6
Crystal structure of an L‐type lectin domain from archaea6
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Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)6
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins6
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Assessment of three‐dimensional RNA structure prediction in CASP156
Lysine Acetylation of Plant α‐Tubulins: Scaling Up the Local Effect to Large System Transformations6
Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes6
Iterated local search with partition crossover for computational protein design6
The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma‐associated herpesvirus protease6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming6
Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers6
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping6
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study6
Issue Information ‐ Forthcoming6
Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking6
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On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification6
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Chemical reactivity and binding interactions in ribonucleic acidpeptide complexes6
TetR and OmpR family regulators in natural product biosynthesis and resistance6
Issue Information ‐ Table of Content5
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction5
Atomistic insight into the luminal allosteric regulation of vesicular glutamate transporter 2 by chloride and protons: An all‐atom molecular dynamics simulation study5
Computational Elucidation of Possible Contributors to Formation and Stabilization of ATP‐Lid Down‐Conformation in the N‐Terminal Domain of Hsp905
Unveiling the biological interface of protein complexes by mass spectrometry‐coupled methods5
ScaffoldMatcher:A CMA‐ESbased algorithm for identifying hotspot aligned peptidomimetic scaffolds5
Predicting mutant outcome by combining deep mutational scanning and machine learning5
Structural Implications of HIV‐1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains5
The following articles for this Special Issue were published in different Issues5
Cover Image, Volume 89, Issue 95
Interplay between hydrogen and chalcogen bonds in cysteine5
Protein folding and unfolding: proline cistrans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel5
Cover Image, Volume 91, Issue 125
The 1.7 Å crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis5
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP155
Structural Insights Into the Impact of the Glycine‐Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase5
Issue Information ‐ Table of Content5
What can AlphaFold do for antimicrobial amyloids?5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding5
The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key Determinants5
Atomic‐level thermodynamics analysis of the binding free energy of SARS‐CoV‐2 neutralizing antibodies5
The Crystal Structure of the Domain of Unknown Function 1480 (DUF1480) From Klebsiella pneumoniae5
Understanding the Role of RING‐Between‐RING E3 Ligase of the Human Malaria Parasite5
Protein aggregates thermodynamically order regardless of sequence5
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