OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design 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 2022-05-01 to 2026-05-01.)

Article	Citations
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	88
Reshaping globular dynamics of S. aureus pyruvate kinase via bond restraints to allosteric sites	48
Impact of physical activity on the hypothalamic–pituitary–gonadal axis in older males: a comparative and AI-based predictive modeling study of demographic factors and stress markers	31
Interconversion of the (+)-O-desmethyltramadol to the lowest-energy conformer when coupled to µ-opioid receptor: comprehensive analysis using in silico molecular modeling	28
Computational peptide discovery with a genetic programming approach	28
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	25
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	25
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	23
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix	21
QM assisted ML for 19F NMR chemical shift prediction	21
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions	20
Multimodal computational approaches coupled with experimental assays to identify flavonoids as potent inhibitors of diabetes and AGEs	20
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	19
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling	18
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	15
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	15
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	14
FastGrow: on-the-fly growing and its application to DYRK1A	14
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells	12
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach	12
Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps	11
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	11
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	11
Design, synthesis, pharmacological evaluation and computational modeling of 4-formyl-2-nitrophenyl quinoline-8-sulfonate derived thiosemicarbazones as antidiabetic agents	11
Harnessing formaldehyde detection: novel metal-doped coronene sensors to combat pollution and enable early lung cancer diagnosis	11

Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	10
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	10
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	10
Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity	10
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	10
Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	10
Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders	9
Improvement of multi-task learning by data enrichment: application for drug discovery	9
In silico development of RNA aptamer candidates against thyroid receptor	9
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	9
Breast cancer diagnosis from histopathological images and molecular signatures by fusing features with an explainable AI-based residual tabular network model	9
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors	9
An overview of the SAMPL8 host–guest binding challenge	9
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	8
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study	8
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	8
User-centric design of a 3D search interface for protein-ligand complexes	8
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	7
Antitumor evaluation of novel alizarin-based derivatives through biological and computational approaches	7
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	7
Advanced investigation of the adsorption process of geosmin molecules on polar bear and camel olfactory receptors: statistical physics treatment, in-depth DFT-modeling, and docking analysis	7
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	7
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	7
DFT and molecular docking-guided investigation of mixed-ligand octahedral Fe(III) and Cu(II) Schiff-base and albendazole complexes with antimicrobial potential	7
Interpretable machine learning-driven QSAR modeling for coagulation factor X inhibitors: from molecular descriptors to predictive potency	7
Effect of emulsion-based nanosystems on the encapsulation behavior of triptorelin using molecular dynamics simulation	7
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	7
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	7
Discovery of potent thymidine phosphorylase inhibitors from Euphorbia pulcherrima Willd. ex Klotzsch with experimental validation and computational analysis	7
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features	7
A large language model-guided reinforcement learning framework for EGFR anticancer drug design	7
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	6
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	6
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	6
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets	6
Artificial intelligence in protein-based detection and inhibition of AMR pathways	6
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor	6
Molecular dynamics insights into the interactions of biocompatible synthetic polymer composites with carbon-based nanoparticle derivatives: a comparative study of PLGA and PCL interactions with GO/rGO	6
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	6
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn	6
Discovery of novel natural product-derived EGFR inhibitors using multiple linear regression, stacked ensemble regression, and fingerprinting approaches	5
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	5
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	5
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	5
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	5
Identification of antidiabetic leads using in-silico screening, molecular dynamics simulation, and biological evaluation using cell viability, anti-adipogenesis, glucose uptake, and peroxisome prolife	5
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	5
Discovery of novel natural compounds as PKCθ inhibitors: structure-based virtual screening and in vitro evaluation	5
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	5
Multi-spatial channel attention and inceptionv3-based CAD system with optimized MLP for lung cancer detection	5

Mycobacterium tuberculosis FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents	5
PBP_ICBA: a prediction of bacterial promoters in specific organisms using an improved convolutional block attention module	5
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles	5
Exploring DrugCentral: from molecular structures to clinical effects	5
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	5
Multi-scale in-silico modelling to unveil structural requirements for DNA-PK inhibitors as radiosensitizers and MolSHAP based design of novel ligands	5
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach	5
Correction: Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design	4
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	4
Predicting drug-target interactions and binding affinity using an optimized deep learning approach	4
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	4
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	4
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	4
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders	4
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	4
From mundane to surprising nonadditivity: drivers and impact on ML models	4
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	4
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy	4
AI-driven peptide discovery for endometrial cancer: deep generative modeling and molecular simulation in the big data era	4
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction q	4
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT	4
Designing novel FAK inhibitors targeting gastric cancer: a combined approach using machine learning, docking analysis, molecular dynamics simulations, and experimental validation	4
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	4
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	4
Comparative assessment of physics-based in silico methods to calculate relative solubilities	4
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	4
Therapeutic potential of [(8-hydroxyquinolin-7-yl)(phenyl)methylamino] benzoic acid regioisomers against human-intoxicating botulinum neurotoxin serotypes: computational modeling to in vivo protection	4
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	4
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	4