OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Computer-Aided Molecular Design is 3. 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 2021-08-01 to 2025-08-01.)

Article	Citations
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	139
Computational peptide discovery with a genetic programming approach	54
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	40
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	23
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	23
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	22
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	19
QM assisted ML for 19F NMR chemical shift prediction	19
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	17
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	16
FastGrow: on-the-fly growing and its application to DYRK1A	16
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	16
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	16
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	15
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	14
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	14
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	14
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	13
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	12
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	11
Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	11
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	11
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	10

Improvement of multi-task learning by data enrichment: application for drug discovery	10
Imputation of sensory properties using deep learning	10
User-centric design of a 3D search interface for protein-ligand complexes	10
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	10
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	9
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	9
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	9
Extended continuous similarity indices: theory and application for QSAR descriptor selection	9
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	9
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	9
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	9
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	9
Contact networks in RNA: a structural bioinformatics study with a new tool	9
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	9
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	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
Comparing classification models—a practical tutorial	8
Comparison of logP and logD correction models trained with public and proprietary data sets	8
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	8
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	8
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	8
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	8
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	8
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	8
Exploring DrugCentral: from molecular structures to clinical effects	8
Comparative assessment of physics-based in silico methods to calculate relative solubilities	7
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT	7
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	7
Turbo prediction: a new approach for bioactivity prediction	7
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	7
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	7
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	6
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders	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
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	6
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	6
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	6
From mundane to surprising nonadditivity: drivers and impact on ML models	6
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	6
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	6
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	6
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy	5
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	5
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	5
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	5
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	5
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective	5
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights	5
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study	5
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	5

Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	5
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	5
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations	5
Thermodynamic free energy map for the non-oxidative glycolysis pathways	4
Correction: Exploring DrugCentral: from molecular structures to clinical effects	4
OPTUNA optimization for predicting chemical respiratory toxicity using ML models	4
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge	4
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction	4
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	4
Quantum algorithm for protein-ligand docking sites identification in the interaction space	4
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	4
Best practices for repurposing studies	4
Is there a common allosteric binding site for G-protein coupled receptors?	4
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	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
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	4
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	4
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	4
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	4
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	4
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	4
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	4
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	4
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium	3
ADis-QSAR: a machine learning model based on biological activity differences of compounds	3
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	3
Rethinking the applicability domain analysis in QSAR models	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
On the force field optimisation of $$\beta$$-lactam cores using the force field Toolkit	3
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability	3
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	3
Convolidine as potent BACE1 inhibitor for Alzheimer’s disease; in-silico coupled with in-vitro assessment	3
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors	3
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation	3
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics	3
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	3