OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design 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 2021-12-01 to 2025-12-01.)

Article	Citations
Computational peptide discovery with a genetic programming approach	166
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	69
Interconversion of the (+)-O-desmethyltramadol to the lowest-energy conformer when coupled to µ-opioid receptor: comprehensive analysis using in silico molecular modeling	42
Reshaping globular dynamics of S. aureus pyruvate kinase via bond restraints to allosteric sites	28
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	23
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix	21
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	21
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions	21
QM assisted ML for 19F NMR chemical shift prediction	20
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	19
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	18
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	18
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	17
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	17
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling	16
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	16
Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps	16
FastGrow: on-the-fly growing and its application to DYRK1A	15
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	15
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	14
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	14
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach	13
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells	12
Design, synthesis, pharmacological evaluation and computational modeling of 4-formyl-2-nitrophenyl quinoline-8-sulfonate derived thiosemicarbazones as antidiabetic agents	11
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	11

Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	10
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	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	10
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	10
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	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
An overview of the SAMPL8 host–guest binding challenge	9
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors	9
In silico development of RNA aptamer candidates against thyroid receptor	9
Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	9
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	9
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study	8
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features	8
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	8
Improvement of multi-task learning by data enrichment: application for drug discovery	8
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	8
Contact networks in RNA: a structural bioinformatics study with a new tool	8
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	8
Breast cancer diagnosis from histopathological images and molecular signatures by fusing features with an explainable AI-based residual tabular network model	8
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	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
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	7
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	7
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	7
Extended continuous similarity indices: theory and application for QSAR descriptor selection	7
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets	7
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	7
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	7
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	7
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	6
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach	6
Artificial intelligence in protein-based detection and inhibition of AMR pathways	6
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	6
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn	6
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	6
Comparison of logP and logD correction models trained with public and proprietary data sets	6
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	6
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	6
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor	6
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	5
From mundane to surprising nonadditivity: drivers and impact on ML models	5
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	5
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	5
Mycobacterium tuberculosis FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents	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
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	5
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	5
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles	5
Comparative assessment of physics-based in silico methods to calculate relative solubilities	5

Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT	5
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	5
Exploring DrugCentral: from molecular structures to clinical effects	5