OOIR: Observatory of International Research

Papers

(The TQCC of Proteins-Structure Function and Bioinformatics is 4. 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 2021-04-01 to 2025-04-01.)

Article	Citations
Assessing the binding properties of CASP14 targets and models	398
The ChaC1 active site: Defining the residues and determining the role of ChaC1‐exclusive residues in the structural and functional stability	312
Issue Information ‐ Forthcoming	272
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules	149
Structural modeling of peptide toxin–ion channel interactions using RosettaDock	135
An updated dataset and a structure‐based prediction model for protein–RNA binding affinity	96
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	64
SARS‐CoV‐2 Mpro Dihedral Angles Reveal Allosteric Signaling	56
Physics‐based protein structure refinement in the era of artificial intelligence	55
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	55
Issue Information ‐ Table of Content	51
Issue Information ‐ Table of Content	51
Issue Information ‐ Forthcoming	50
Scoring of protein–protein docking models utilizing predicted interface residues	47
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	43
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	42
ComparePD: Improving protein–DNA complex model comparison with hydrogen bond energy‐based metrics	42
Investigating the functional role of a buried interchain aromatic cluster in Escherichia coli GrpE dimer	42
Characterization of the E26H Mutant Schistosoma japonicum Glutathione S‐Transferase	41
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	41
Cover Image, Volume 91, Issue 12	40
Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies	37
Flattening the curve—How to get better results with small deep‐mutational‐scanning datasets	35
Issue Information ‐ Forthcoming	34
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	33

Cover Image, Volume 90, Issue 1	33
Cover Image, Volume 90, Issue 1	33
Analysis of CheW‐like domains provides insights into organization of prokaryotic chemotaxis systems	30
Cover Image, Volume 89, Issue 12	30
Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	30
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iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	29
Targeting protein tyrosine phosphatase 1B in obesity‐associated colon cancer: Possible role of sweet potato (Ipomoea batatas)	29
Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and t	27
An interaction network in Bacillus subtilis coproporphyrinogen oxidase is essential for the oxidation of protoporphyrinogen IX	27
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	27
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	26
Cover Image, Volume 90, Issue 11	26
Issue Information ‐ Forthcoming	26
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	24
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	24
Issue Information ‐ Table of Content	23
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	23
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Issue Information ‐ Table of Content	21
QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study	20
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	20
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods	20
Issue Information ‐ Forthcoming	20
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	19
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	19
Fundamentals behind the specificity of Cysteinyl‐tRNA synthetase: MD and QM/MM joint investigations	19
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	18
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis	18
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	17
Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition	17
Issue Information ‐ Table of Content	16
Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin‐1	16
Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms	16
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	16
Boosting the analysis of protein interfaces with multiple interface string alignments: Illustration on the spikes of coronaviruses	16
Ligands‐induced open‐close conformational change during DapE catalysis: Insights from molecular dynamics simulations	15
Dynamics in an unusual acyl carrier protein from a ladderane lipid‐synthesizing organism	15
Lessons on protein structure from interleukin‐4: All disulfides are not created equal	14
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	14
Issue Information ‐ Table of Content	14
Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi	14
Entropy‐based distance cutoff for protein internal contact networks	14
Protein structuromics: A new method for protein structure–function crosstalk in glioma	14
Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular dynamics simulations	14
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	14
New simulation insights on the structural transition mechanism of bovine rhodopsin activation	13
Insight into substrate‐assisted catalytic mechanism and stereoselectivity of bifunctional nocardicin thioesterase	13
Issue Information ‐ Table of Content	13
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Issue Information ‐ Forthcoming	12
Total free energy analysis of fully hydrated proteins	12
Issue Information ‐ Table of Content	12
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Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations	12
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Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	12
ACE2‐based decoy receptors for SARS coronavirus 2	11
RosettaCM for antibodies with very long HCDR3s and low template availability	11
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	11
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	10
Issue Information ‐ Table of Content	10
Simpler Protein Domain Identification Using Spectral Clustering	10
Issue Information ‐ Table of Content	10
Insights Into the Molecular Interactions of MIC2 and M2AP: Role of TSR6 and Conservation Across Species	10
Unraveling the Structural Basis of Biased Agonism in the β₂‐Adrenergic Receptor Through Molecular Dynamics Simulations	10
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	9
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	9
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	9
Energetic and structural insights behind calcium induced conformational transition in calmodulin	9
Structural Classification Insights Into the Plant Defensive Peptides	9
Graphical models for identifying pore‐forming proteins	9
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	9
The study of iron‐ and copper‐binding proteome of Fusarium oxysporum and its effector candidates	8
Dimerization underlies the aggregation propensity of intrinsically disordered coiled‐coil domain‐containing 124	8
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic	8
Inferring metal binding sites in flexible regions of proteins	8
Protein oligomer structure prediction using GALAXY in CASP14	8
Plastic structures for diverse substrates: A revisit of human ABC transporters	8
Structural and Biochemical Analysis of Butanol Dehydrogenase From Thermotoga maritima	8
The energetics and evolution of oxidoreductases in deep time	8
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	8
Rational design of antibody‐like peptides for targeting the human complement fragment protein C5a	8
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	8
Allosteric pathways of SARS and SARS‐CoV‐2 spike protein identified by neural relational inference	7
Construction of dynamic protein interaction network based on gene expression data and quartile one principle	7
A study of a hierarchical structure of proteins and ligand binding sites of receptors using the triangular spatial relationship‐based structure comparison method and development of a size‐filtering fe	7
Assessing the utility of CASP14 models for molecular replacement	7
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	7
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	7
FTDMP: A Framework for Protein–Protein, Protein–DNA, and Protein–RNA Docking and Scoring	7
Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation	7
A novel consensus‐based computational pipeline for screening of antibody therapeutics for efficacy against SARS‐CoV‐2 variants of concern including Omicron variant	7
High‐accuracy protein structure prediction in CASP14	7
Towards a Greener AlphaFold2 Protocol for Antibody–Antigen Modeling: Insights From CAPRI Round 55	7
PCANN Program for Structure‐Based Prediction of Protein–Protein Binding Affinity: Comparison With Other Neural‐Network Predictors	7
Unraveling the role of flexible coil near calcium binding site of levansucrase on thermostability and product profile via proline substitution and molecular dynamics simulations	7
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	7
Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective	7
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	7
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Structures of MERS‐CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and CHARMM36m and AMBER99SB force field para	6
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease	6
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Applying and improving AlphaFold at CASP14	6
Secondary structure and toxicity of lysozyme fibrils are determined by the length and unsaturation of phosphatidic acid	6
In memoriam of Narayanaswamy Srinivasan (1962–2021)	6
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides	6
Issue Information ‐ Table of Content	6
A computational approach to investigate constitutive activation of NF‐κB	6
Issue Information ‐ Forthcoming	6
Issue Information ‐ Forthcoming	6
The role of leucine and isoleucine in tuning the hydropathy of class A GPCRs	6
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	6
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	6
Correction to “Allosteric Modulation of Fluorescence Revealed by Hydrogen Bond Dynamics in a Genetically Encoded Maltose Biosensor”	6
Molecular insights into the differential efflux mechanism of Rv1634 protein, a multidrug transporter of major facilitator superfamily in Mycobacterium tuberculosis	6
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	6
Cover Image, Volume 90, Issue 2	6
Crystal structure of reducing‐end xylose‐releasing exoxylanase in subfamily 7 of glycoside hydrolase family 30	6
Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor	6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	6
Recent progress in the structural biology of P2X receptors	6
Predicting protein flexibility with AlphaFold	6
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	6
Structure of the Complex of Lactoperoxidase With Nitric Oxide at 1.95 Å Resolution	6
Skittles: GNN‐Assisted Pseudo‐Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction	6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	5
Cover Image, Volume 89, Issue 11	5

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Structure and elasticity of healthy and Alzheimer's disease cell membranes revealed by molecular dynamics simulations	5
Issue Information ‐ Table of Content	5
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	5
GABA receptor associated protein changes the electrostatic environment around the GABA type A receptor	5
Cover Image, Volume 92, Issue 8	5
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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	5
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	5
Iterated local search with partition crossover for computational protein design	5
Crystal structure of O‐ureidoserine racemase found in the d‐cycloserine biosynthetic pathway	5
A novel chimeric protein with enhanced cytotoxic effects on breast cancer in vitro and in vivo	5
Issue Information ‐ Forthcoming	5
MEM‐FET: Essential protein prediction using membership feature and machine learning approach	5
Crystal structure of Bak bound to the BH3 domain of Bnip5, a noncanonical BH3 domain‐containing protein	5
A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface	5
Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative	5
Issue Information ‐ Table of Content	5
Issue Information ‐ Table of Content	5
Structure memes: Intuitive visualization of sequence logo and subfamily logo information in a 3D protein‐structural context	5
Cover Image, Volume 89, Issue 9	5
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	5
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	5
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	5
Issue Information ‐ Forthcoming	5
Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF	5
On the diversity of F₄₂₀‐dependent oxidoreductases: A sequence‐ and structure‐based classification	5
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	5
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Crystal structure ofAspergillus fumigatusAroH, an aromatic amino acid aminotransferase	5
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	5
Expression and immobilization of trypsin‐like domain of serine protease from Pseudomonas aeruginosa for improved stability and catalytic activity	5
A C‐term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions	4
Issue Information ‐ Forthcoming	4
State‐dependent dynamics of extramembrane domains in the β₂‐adrenergic receptor	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases	4
Empowering canonical biochemicals with cross‐linked novelty: Recursions in applications of protein cross‐links	4
Crystal structure of an L‐type lectin domain from archaea	4
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	4
Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	4
Unraveling the Molecular Architecture of Mosquito D1‐Like Dopamine Receptors: Insights Into Ligand Binding and Structural Dynamics for Insecticide Development	4
Evaluation of model refinement in CASP14	4
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	4
Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches	4
Issue Information ‐ Forthcoming	4
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	4
FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins	4
Structure–function relationships in ShKT domain peptides: ShKT‐Ts1 from the sea anemone Telmatactis stephensoni	4
A computer aided drug discovery based discovery of lead‐like compounds against KDM5A for cancers using pharmacophore modeling and high‐throughput virtual screening	4
Computational analysis of propeptide‐containing proteins and prediction of their post‐cleavage conformation changes	4
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Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	4
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	4
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	4
Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	4
Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data	4
Proteome analysis of the circadian clock protein PERIOD2	4
Issue Information ‐ Forthcoming	4
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	4
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	4
Mutual information analysis of mutation, nonlinearity, and triple interactions in proteins	4
II. Geometrical framework for thinking about globular proteins: The power of poking	4
Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences	4
Specific recognition between YTHDF3 and m⁶A‐modified RNA: An all‐atom molecular dynamics simulation study	4
Comparative protein structure network analysis on 3CL^pro from SARS‐CoV‐1 and SARS‐CoV‐2	4
Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site‐directed mutagenesis	4
Crystal structure of the dimerized of porcine circovirus type II replication‐related protein Rep′	4
Structural basis for binding of the renal carcinoma target hypoxia‐inducible factor 2α to prolyl hydroxylase domain 2	4
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	4