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 2021-02-01 to 2025-02-01.)

Article	Citations
Assessing the binding properties of CASP14 targets and models	365
The ChaC1 active site: Defining the residues and determining the role of ChaC1‐exclusive residues in the structural and functional stability	286
Issue Information ‐ Forthcoming	252
Issue Information ‐ Forthcoming	126
Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules	112
Structural modeling of peptide toxin–ion channel interactions using RosettaDock	85
An updated dataset and a structure‐based prediction model for protein–RNA binding affinity	52
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	51
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	51
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	50
Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods	42
Issue Information ‐ Table of Content	40
Physics‐based protein structure refinement in the era of artificial intelligence	40
Issue Information ‐ Table of Content	39
Scoring of protein–protein docking models utilizing predicted interface residues	36
Issue Information ‐ Forthcoming	36
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation	35
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	35
Investigating the functional role of a buried interchain aromatic cluster in Escherichia coli GrpE dimer	33
ComparePD: Improving protein–DNA complex model comparison with hydrogen bond energy‐based metrics	33
Issue Information ‐ Forthcoming	32
Cover Image, Volume 90, Issue 1	31
Analysis of CheW‐like domains provides insights into organization of prokaryotic chemotaxis systems	30
Cover Image, Volume 89, Issue 12	30
Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus	30

Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor	30
Cover Image, Volume 90, Issue 1	30
	29
iNucRes‐ASSH: Identifying nucleic acid‐binding residues in proteins by using self‐attention‐based structure‐sequence hybrid neural network	27
Targeting protein tyrosine phosphatase 1B in obesity‐associated colon cancer: Possible role of sweet potato (Ipomoea batatas)	27
Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and t	26
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	25
Cover Image, Volume 90, Issue 11	24
An interaction network in Bacillus subtilis coproporphyrinogen oxidase is essential for the oxidation of protoporphyrinogen IX	24
Flattening the curve—How to get better results with small deep‐mutational‐scanning datasets	23
Thermodynamic stabilization of von Willebrand factor A1 domain induces protein loss of function	23
Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective	23
Issue Information ‐ Forthcoming	23
	22
Issue Information ‐ Table of Content	22
Issue Information ‐ Table of Content	21
Issue Information ‐ Forthcoming	21
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	20
Conformational diversity defines substrate specificity of thymidylate/uridylate kinase from Candida albicans	20
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study	20
QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study	19
Secondary structure and toxicity of lysozyme fibrils are determined by the length and unsaturation of phosphatidic acid	19
Mask blast with a new chemical logic of amino acids for improved protein function prediction	19
Fundamentals behind the specificity of Cysteinyl‐tRNA synthetase: MD and QM/MM joint investigations	18
Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods	18
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	17
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	17
Structure–sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis	16
Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin‐1	16
Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition	16
rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation	16
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	16
Issue Information ‐ Table of Content	15
Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms	15
Boosting the analysis of protein interfaces with multiple interface string alignments: Illustration on the spikes of coronaviruses	15
Protein structuromics: A new method for protein structure–function crosstalk in glioma	14
Ligands‐induced open‐close conformational change during DapE catalysis: Insights from molecular dynamics simulations	14
Lessons on protein structure from interleukin‐4: All disulfides are not created equal	14
Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular dynamics simulations	14
Dynamics in an unusual acyl carrier protein from a ladderane lipid‐synthesizing organism	14
Analyzing the cation‐aromatic interactions in proteins: Cation‐aromatic database V2.0	14
Issue Information ‐ Table of Content	14
Community analysis of large‐scale molecular dynamics simulations elucidated dynamics‐driven allostery in tyrosine kinase 2	14
Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi	13
Entropy‐based distance cutoff for protein internal contact networks	13
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	13
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	13
Issue Information ‐ Table of Content	12
	12
	12

New simulation insights on the structural transition mechanism of bovine rhodopsin activation	12
Insight into substrate‐assisted catalytic mechanism and stereoselectivity of bifunctional nocardicin thioesterase	12
Issue Information ‐ Table of Content	11
	11
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues	10
Issue Information ‐ Table of Content	10
RosettaCM for antibodies with very long HCDR3s and low template availability	10
Issue Information ‐ Forthcoming	10
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	10
Insights Into the Molecular Interactions of MIC2 and M2AP: Role of TSR6 and Conservation Across Species	10
Cover Image, Volume 91, Issue 12	10
Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations	10
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	10
Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species	10
Graphical models for identifying pore‐forming proteins	10
Energetic and structural insights behind calcium induced conformational transition in calmodulin	9
The energetics and evolution of oxidoreductases in deep time	9
Oxygen‐insensitive nitroreductase E. coliNfsA, but not NfsB, is inhibited by fumarate	9
Characterization and Inhibition of the Chaperone Function of Plasmodium falciparum Glucose‐Regulated Protein 94 kDa (PfGrp94)	9
HSV‐1 ICP0 dimer domain adopts a novel β‐barrel fold	9
Protein structure search to support the development of protein structure prediction methods	9
The study of iron‐ and copper‐binding proteome of Fusarium oxysporum and its effector candidates	9
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	9
Unraveling the role of flexible coil near calcium binding site of levansucrase on thermostability and product profile via proline substitution and molecular dynamics simulations	9
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	9
Protein oligomer structure prediction using GALAXY in CASP14	9
Applying and improving AlphaFold at CASP14	9
Dimerization underlies the aggregation propensity of intrinsically disordered coiled‐coil domain‐containing 124	8
Predicting protein flexibility with AlphaFold	8
Rational design of antibody‐like peptides for targeting the human complement fragment protein C5a	8
Total free energy analysis of fully hydrated proteins	8
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	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
Plastic structures for diverse substrates: A revisit of human ABC transporters	8
Recent progress in the structural biology of P2X receptors	8
Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies	8
Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol	7
Structural and Biochemical Analysis of Butanol Dehydrogenase From Thermotoga maritima	7
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	7
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	7
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	7
Mechanistic understanding of bacterial FAALs and the role of their homologs in eukaryotes	7
Unraveling the Structural Basis of Biased Agonism in the β₂‐Adrenergic Receptor Through Molecular Dynamics Simulations	7
Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective	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
ACE2‐based decoy receptors for SARS coronavirus 2	7
High‐accuracy protein structure prediction in CASP14	7
Construction of dynamic protein interaction network based on gene expression data and quartile one principle	7
Structural Classification Insights Into the Plant Defensive Peptides	7
Allosteric pathways of SARS and SARS‐CoV‐2 spike protein identified by neural relational inference	7
FTDMP: A Framework for Protein–Protein, Protein–DNA, and Protein–RNA Docking and Scoring	7
Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases	7
Assessing the utility of CASP14 models for molecular replacement	7
An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast‐two‐hybrid screening data	6
DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides	6
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	6
	6
Comparative analysis of permanent and transient domain–domain interactions in multi‐domain proteins	6
	6
Cover Image, Volume 90, Issue 2	6
Molecular insights into the differential efflux mechanism of Rv1634 protein, a multidrug transporter of major facilitator superfamily in Mycobacterium tuberculosis	6
Structure of the Complex of Lactoperoxidase With Nitric Oxide at 1.95 Å Resolution	6
Estimation of model accuracy in CASP15 using the ModFOLDdock server	6
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints	6
Crystal structure of reducing‐end xylose‐releasing exoxylanase in subfamily 7 of glycoside hydrolase family 30	6
In memoriam of Narayanaswamy Srinivasan (1962–2021)	6
Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation	6
The role of leucine and isoleucine in tuning the hydropathy of class A GPCRs	6
Issue Information ‐ Forthcoming	6
Crystal structure ofAspergillus fumigatusAroH, an aromatic amino acid aminotransferase	6
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins	6
A computational approach to investigate constitutive activation of NF‐κB	6
Crystal structure of GTP‐dependent dephospho‐coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis	6
Structure of MeuNaTxα‐1 toxin from scorpion venom highlights the importance of the nest motif	6
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods	6
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	6
ProBAN: Neural network algorithm for predicting binding affinity in protein–protein complexes	6
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming	6
Characterization of the E26H Mutant Schistosoma japonicum Glutathione S‐Transferase	6

Issue Information ‐ Forthcoming	6
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
GABA receptor associated protein changes the electrostatic environment around the GABA type A receptor	6
Structural Basis for the Essential Role of Ca²⁺ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin‐Resistant Staphylococcus aur	6
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination	6
Issue Information ‐ Table of Content	6
	5
A novel chimeric protein with enhanced cytotoxic effects on breast cancer in vitro and in vivo	5
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	5
A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface	5
Location of S‐nitrosylated cysteines in protein three‐dimensional structures	5
Issue Information ‐ Forthcoming	5
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
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
Cover Image, Volume 89, Issue 4	5
Issue Information ‐ Table of Content	5
Cover Image, Volume 89, Issue 9	5
Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative	5
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	5
On the diversity of F₄₂₀‐dependent oxidoreductases: A sequence‐ and structure‐based classification	5
Issue Information ‐ Table of Content	5
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	5
Expression and immobilization of trypsin‐like domain of serine protease from Pseudomonas aeruginosa for improved stability and catalytic activity	5
Structure memes: Intuitive visualization of sequence logo and subfamily logo information in a 3D protein‐structural context	5
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	5
Surveying nonvisual arrestins reveals allosteric interactions between functional sites	5
Issue Information ‐ Table of Content	5
Cover Image, Volume 89, Issue 11	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
Cover Image, Volume 92, Issue 8	5
	5
Issue Information ‐ Forthcoming	5
Dynamical changes of SARS‐CoV‐2 spike variants in the highly immunogenic regions impact the viral antibodies escaping	5
Convolutional ProteinUnetLM competitive with long short‐term memory‐based protein secondary structure predictors	5
Crystal structure of Bak bound to the BH3 domain of Bnip5, a noncanonical BH3 domain‐containing protein	5
	5
A computer aided drug discovery based discovery of lead‐like compounds against KDM5A for cancers using pharmacophore modeling and high‐throughput virtual screening	4
Unraveling the Molecular Architecture of Mosquito D1‐Like Dopamine Receptors: Insights Into Ligand Binding and Structural Dynamics for Insecticide Development	4
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
Issue Information ‐ Forthcoming	4
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	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
Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	4
Constitutive expression and discovery of antimicrobial peptides in Zygogramma bicolorata (Coleoptera: Chrysomelidae)	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Structure–function relationships in ShKT domain peptides: ShKT‐Ts1 from the sea anemone Telmatactis stephensoni	4
Improving protein structure prediction with extended sequence similarity searches and deep‐learning‐based refinement in CASP15	4
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	4
Assessment of three‐dimensional RNA structure prediction in CASP15	4
Molecular dynamics study reveals key disruptors of MEIG1–PACRG interaction	4
The high identity of the Trypanosoma cruziGroup‐I of trans‐sialidases points them as promising vaccine immunogens	4
FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins	4
Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data	4
Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches	4
RNA tertiary structure modeling with BRiQ potential in CASP15	4
Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases	4
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	4
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units	4
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	4
Crystal structure of the dimerized of porcine circovirus type II replication‐related protein Rep′	4
New tyrosinases with putative action against contaminants of emerging concern	4
New prediction categories in CASP15	4
Issue Information ‐ Forthcoming	4
Reframing prosegment‐dependent folding and limits on natural protein folding landscapes from an evolutionary perspective	4
Proteome analysis of the circadian clock protein PERIOD2	4
PDB‐BRE: A ligand–protein interaction binding residue extractor based on Protein Data Bank	4
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	4
Evaluation of model refinement in CASP14	4
Mutual information analysis of mutation, nonlinearity, and triple interactions in proteins	4
Assessment of protein–ligand complexes in CASP15	4
	4
New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study	4