Journal of Computer-Aided Molecular Design

Article	Citations
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	101
Computational peptide discovery with a genetic programming approach	54
Reshaping globular dynamics of S. aureus pyruvate kinase via bond restraints to allosteric sites	35
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	31
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	31
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix	28
Interconversion of the (+)-O-desmethyltramadol to the lowest-energy conformer when coupled to µ-opioid receptor: comprehensive analysis using in silico molecular modeling	28
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling	25
QM assisted ML for 19F NMR chemical shift prediction	22
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	22
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	21
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	21
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	20
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	19
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions	18
Multimodal computational approaches coupled with experimental assays to identify flavonoids as potent inhibitors of diabetes and AGEs	17
Design, synthesis, pharmacological evaluation and computational modeling of 4-formyl-2-nitrophenyl quinoline-8-sulfonate derived thiosemicarbazones as antidiabetic agents	16
Harnessing formaldehyde detection: novel metal-doped coronene sensors to combat pollution and enable early lung cancer diagnosis	16
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	15
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells	12
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	12
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	12
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	11
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach	11
Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps	11

FastGrow: on-the-fly growing and its application to DYRK1A	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
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	11
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	10
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	10
In silico development of RNA aptamer candidates against thyroid receptor	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
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors	10
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	9
Breast cancer diagnosis from histopathological images and molecular signatures by fusing features with an explainable AI-based residual tabular network model	9
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	9
Evaluating computational and experimental approaches in early-stage Alzheimer’s drug discovery: a systematic review	9
An overview of the SAMPL8 host–guest binding challenge	9
User-centric design of a 3D search interface for protein-ligand complexes	9
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	8
Improvement of multi-task learning by data enrichment: application for drug discovery	8
Antitumor evaluation of novel alizarin-based derivatives through biological and computational approaches	8
Interpretable machine learning-driven QSAR modeling for coagulation factor X inhibitors: from molecular descriptors to predictive potency	8
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study	8
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	8
DFT and molecular docking-guided investigation of mixed-ligand octahedral Fe(III) and Cu(II) Schiff-base and albendazole complexes with antimicrobial potential	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
Discovery of potent thymidine phosphorylase inhibitors from Euphorbia pulcherrima Willd. ex Klotzsch with experimental validation and computational analysis	8
Effect of emulsion-based nanosystems on the encapsulation behavior of triptorelin using molecular dynamics simulation	8
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features	8
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	8
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	7
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study	7
A large language model-guided reinforcement learning framework for EGFR anticancer drug design	7
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	7
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	7
Mycobacterium tuberculosis FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents	7
Artificial intelligence in protein-based detection and inhibition of AMR pathways	7
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	7
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	7
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	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
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	7
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	7
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets	7
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor	7
Identification of antidiabetic leads using in-silico screening, molecular dynamics simulation, and biological evaluation using cell viability, anti-adipogenesis, glucose uptake, and peroxisome prolife	6
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	6
Discovery of novel natural compounds as PKCθ inhibitors: structure-based virtual screening and in vitro evaluation	6
PBP_ICBA: a prediction of bacterial promoters in specific organisms using an improved convolutional block attention module	6
Discovery of novel natural product-derived EGFR inhibitors using multiple linear regression, stacked ensemble regression, and fingerprinting approaches	6
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	6
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	6
Multi-scale in-silico modelling to unveil structural requirements for DNA-PK inhibitors as radiosensitizers and MolSHAP based design of novel ligands	6

In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	5
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	5
Multi-spatial channel attention and inceptionv3-based CAD system with optimized MLP for lung cancer detection	5
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	5
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles	5
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	5
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	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	5
Exploring DrugCentral: from molecular structures to clinical effects	5
Predicting drug-target interactions and binding affinity using an optimized deep learning approach	5
From mundane to surprising nonadditivity: drivers and impact on ML models	5
Comparative assessment of physics-based in silico methods to calculate relative solubilities	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	4
Calibrating the gap: a user-friendly aqueous $$\text{p}K_a$$ prediction protocol for organic acids, alcohols, and amines	4
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	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
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	4
Designing novel FAK inhibitors targeting gastric cancer: a combined approach using machine learning, docking analysis, molecular dynamics simulations, and experimental validation	4
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	4
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy	4
Theoretical insights into the optoelectronic and charge-transfer characteristics of 5-(1H-1,2,4-triazol-1-yl)-2-thiophenecarboxylic acid	4
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights	4
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations	4
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy	4
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	4
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	4
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	4
AI-driven peptide discovery for endometrial cancer: deep generative modeling and molecular simulation in the big data era	4
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	4
μOR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification	4
Multitarget-directed ligands in Alzheimer’s disease: identification of AChE and BACE1 inhibitors by in silico approaches	4
Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods	4
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective	4
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	4
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders	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
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	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
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	4
Thermodynamic free energy map for the non-oxidative glycolysis pathways	3
OPTUNA optimization for predicting chemical respiratory toxicity using ML models	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
Quantum algorithm for protein-ligand docking sites identification in the interaction space	3
Design, synthesis, and integrated in silico analysis of novel difluoroboron curcumin analogues as potent inhibitors of the K562 leukemia cell line	3
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	3
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study	3
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	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
Investigating the ameliorative effect of Kalanchoe pinnata on neuroinflammation-associated Alzheimer’s disease using network pharmacology, molecular docking, and in vitro studies	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
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	3
HCV genotyping and rational computational designing of an immunogenic multiepitope vaccine against genotype 3a	3
Integrative design and optimization of bioactive schiff bases using computational intelligence and molecular modeling	3
Assessment of quantum chemical predictors for anti-colorectal cancer agents using QSAR modeling	3
Evaluation of novel topiramate–phenolic acid conjugates as potent pancreatic α-amylase inhibitors: in vitro and in silico insights	3
Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design	3
Ultrasonication-assisted green synthesis, in silico EGFR-binding analysis, and cytotoxic evaluation of nitro-perimidines for non-small cell lung cancer	3
Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma	3
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	3
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	3
Computational prioritization of multi-target inhibitors: explainable QSAR and docking-based discovery of dual AChE/BACE1 chemotypes	3
Medt5-bi: bidirectional translation between drug indications and molecular structures using a chemically-aware transformer	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
Gene-based lung cancer detection system through omix data and optimized convolutional neural network	2
On the relevance of query definition in the performance of 3D ligand-based virtual screening	2
Pistagremic acid from Pistacia integerrima as a natural multi-target candidate tackling crucial enzymes involved in Alzheimer’s disease	2
Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules	2
Rethinking the applicability domain analysis in QSAR models	2
AI-powered IC50 prediction for p53 inhibitors drug-target interaction via hybrid graph neural networks	2
Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation	2
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics	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
Structure-based design of alicyclic fused pyrazole derivatives for targeting TGF-β receptor I kinase: molecular docking and dynamics insights	2
Machine Learning–Integrated Pharmacophore, DFT Analysis, and molecular dynamics of Diosmetin as a potent ache inhibitor with neuroprotective activity in a Scopolamine-Induced alzheimer’s zebrafish mod	2
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability	2
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity	2
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	2
Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding	2
Ligand and structure-based toxicological assessment of (thio)semicarbazones on cholinesterases	2

Jervine-induced suppression of triple-negative breast cancer (TNBC) cells growth through the regulation of Wnt signaling pathway- an in-silico and in-vitro approach	2
Molecular dynamics modeling and spectroscopic property prediction of V-type nerve agents for safe handling	2
Deep learning model for activity cliffs prediction: a comprehensive approach to protein kinase inhibitors	2
Synthesis, characterization and density functional theory of a novel dichloro(2-(1-anthracene-9-ylmethyl)-1H-1,2,3-triazole-5-yl) pyridine)Cu(II) and polymeric dichloro(2-(1-anthracene-9-ylmethyl)-1H-	2
ADis-QSAR: a machine learning model based on biological activity differences of compounds	2
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	2
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	2
A Multimodal deep learning method for predicting drug-induced liver injury using structural and sequential molecular representations	2
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis	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
Convolidine as potent BACE1 inhibitor for Alzheimer’s disease; in-silico coupled with in-vitro assessment	2
Computational characterization and machine learning analysis of quantum optimized marine fungal metabolites targeting PD-L1 in cancer immunotherapy	2
Multidimensional in silico evaluation of fluorine-18 radiopharmaceuticals: integrating pharmacokinetics, ADMET, and clustering for diagnostic stratification	2
Comparing massively-multitask regression algorithms for drug discovery	2
A coordinative partnership in tungsten chemistry: N-bound isothiocyanate and a tridentate pyrazolone-Schiff base in a hexacoordinate [WO2]2+ complex revealed by DFT and spectroscopy	2
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium	2