OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Computer-Aided Molecular Design is 2. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Computational peptide discovery with a genetic programming approach	163
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	66
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	41
Interconversion of the (+)-O-desmethyltramadol to the lowest-energy conformer when coupled to µ-opioid receptor: comprehensive analysis using in silico molecular modeling	27
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	23
QM assisted ML for 19F NMR chemical shift prediction	20
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix	20
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	20
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	19
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	18
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	18
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions	18
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	17
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
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling	16
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	14
FastGrow: on-the-fly growing and its application to DYRK1A	14
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	14
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	14
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	13
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	12
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells	12
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	11
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	10

Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	10
In silico development of RNA aptamer candidates against thyroid receptor	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	10
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	10
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	10
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors	10
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	9
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	9
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	9
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	9
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	9
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
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	8
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features	8
Contact networks in RNA: a structural bioinformatics study with a new tool	8
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	8
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	8
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	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	8
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets	8
Extended continuous similarity indices: theory and application for QSAR descriptor selection	8
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	7
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	7
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	7
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	7
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	7
Comparison of logP and logD correction models trained with public and proprietary data sets	7
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	7
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn	7
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach	7
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	6
Comparative assessment of physics-based in silico methods to calculate relative solubilities	6
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	6
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	6
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	6
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles	6
Exploring DrugCentral: from molecular structures to clinical effects	6
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	6
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	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
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	5
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy	5
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	5
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	5
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	5
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders	5

From mundane to surprising nonadditivity: drivers and impact on ML models	5
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	5
Turbo prediction: a new approach for bioactivity prediction	5
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	5
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	5
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	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
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations	4
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	4
μOR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification	4
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective	4
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	4
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights	4
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	4
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy	4
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations	4
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	4
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	4
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	4
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study	4
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	4
Best practices for repurposing studies	3
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	3
Thermodynamic free energy map for the non-oxidative glycolysis pathways	3
Prospects for the structure‒function evolution of SARS-CoV-2 main protease inhibitors	3
Correction: Exploring DrugCentral: from molecular structures to clinical effects	3
An in-vitro and in-silico approaches in exploring the molecular contact of COVID-19 antiviral drug molnupiravir with human serum albumin: effect of binding on protein structure	3
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	3
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	3
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	3
OPTUNA optimization for predicting chemical respiratory toxicity using ML models	3
Is there a common allosteric binding site for G-protein coupled receptors?	3
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	3
Quantum algorithm for protein-ligand docking sites identification in the interaction space	3
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	3
Synthesis, TD-DFT calculations, molecular docking and ADME studies of new spiro-oxindole derivatives containing 5(4H)-oxazolone as anti-viral and anti-bacterial agents	3
Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7	2
Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design	2
ADis-QSAR: a machine learning model based on biological activity differences of compounds	2
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics	2
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	2
Multidimensional in silico evaluation of fluorine-18 radiopharmaceuticals: integrating pharmacokinetics, ADMET, and clustering for diagnostic stratification	2
Structure-based design of alicyclic fused pyrazole derivatives for targeting TGF-β receptor I kinase: molecular docking and dynamics insights	2
On the force field optimisation of $$\beta$$-lactam cores using the force field Toolkit	2
Investigating the ameliorative effect of Kalanchoe pinnata on neuroinflammation-associated Alzheimer’s disease using network pharmacology, molecular docking, and in vitro studies	2
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	2
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	2
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations	2
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability	2
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation	2
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium	2
Assembling of phenyl substituted halogens in the C3-position of substituted isatins by mono wave assisted synthesis: development of a new class of monoamine oxidase inhibitors	2
On the relevance of query definition in the performance of 3D ligand-based virtual screening	2
Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules	2
Molecular dynamics modeling and spectroscopic property prediction of V-type nerve agents for safe handling	2
Rethinking the applicability domain analysis in QSAR models	2
Convolidine as potent BACE1 inhibitor for Alzheimer’s disease; in-silico coupled with in-vitro assessment	2