OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design is 6. 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 2021-09-01 to 2025-09-01.)

Article	Citations
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	147
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	57
Computational peptide discovery with a genetic programming approach	40
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	25
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	23
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	22
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	20
QM assisted ML for 19F NMR chemical shift prediction	19
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	19
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	17
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	16
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	16
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	16
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	16
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	15
FastGrow: on-the-fly growing and its application to DYRK1A	14
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	14
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	14
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	13
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	12
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	11
Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	11
An overview of the SAMPL8 host–guest binding challenge	11
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
Improvement of multi-task learning by data enrichment: application for drug discovery	10

Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	10
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	10
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	10
Imputation of sensory properties using deep learning	10
User-centric design of a 3D search interface for protein-ligand complexes	10
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	9
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	9
Extended continuous similarity indices: theory and application for QSAR descriptor selection	9
Contact networks in RNA: a structural bioinformatics study with a new tool	9
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	9
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	9
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	9
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	9
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	9
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	9
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets	8
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach	8
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	8
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	8
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	8
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	8
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	8
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	8
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	7
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	7
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	7
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn	7
Comparing classification models—a practical tutorial	7
Exploring DrugCentral: from molecular structures to clinical effects	7
Comparison of logP and logD correction models trained with public and proprietary data sets	7
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	6
Turbo prediction: a new approach for bioactivity prediction	6
From mundane to surprising nonadditivity: drivers and impact on ML models	6
Comparative assessment of physics-based in silico methods to calculate relative solubilities	6
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	6
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	6
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	6
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	6
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	6
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	6
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT	6