Journal of Computer-Aided Molecular Design

Article	Citations
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	176
Reshaping globular dynamics of S. aureus pyruvate kinase via bond restraints to allosteric sites	72
Interconversion of the (+)-O-desmethyltramadol to the lowest-energy conformer when coupled to µ-opioid receptor: comprehensive analysis using in silico molecular modeling	44
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	28
Computational peptide discovery with a genetic programming approach	25
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix	23
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions	22
QM assisted ML for 19F NMR chemical shift prediction	21
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	20
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	20
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	19
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	18
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	18
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	18
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling	18
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
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	16
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach	15
Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps	15
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells	14
Design, synthesis, pharmacological evaluation and computational modeling of 4-formyl-2-nitrophenyl quinoline-8-sulfonate derived thiosemicarbazones as antidiabetic agents	13
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation	12
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	12
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	11

Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	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
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation	10
In silico development of RNA aptamer candidates against thyroid receptor	10
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors	10
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors	10
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	10
User-centric design of a 3D search interface for protein-ligand complexes	9
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	9
Breast cancer diagnosis from histopathological images and molecular signatures by fusing features with an explainable AI-based residual tabular network model	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
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	9
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	9
Improvement of multi-task learning by data enrichment: application for drug discovery	8
Contact networks in RNA: a structural bioinformatics study with a new tool	8
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones	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
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	8
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study	8
Antitumor evaluation of novel alizarin-based derivatives through biological and computational approaches	8
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	8
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features	8
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease	8
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
Comparison of logP and logD correction models trained with public and proprietary data sets	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
Extended continuous similarity indices: theory and application for QSAR descriptor selection	7
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	7
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation	7
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	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
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	7
Discovery of novel natural product-derived EGFR inhibitors using multiple linear regression, stacked ensemble regression, and fingerprinting approaches	6
Mycobacterium tuberculosis FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents	6
Artificial intelligence in protein-based detection and inhibition of AMR pathways	6
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	6
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches	6
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles	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
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn	6
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor	6
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	6
Multi-scale in-silico modelling to unveil structural requirements for DNA-PK inhibitors as radiosensitizers and MolSHAP based design of novel ligands	5
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 DrugCentral: from molecular structures to clinical effects	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
Comparative assessment of physics-based in silico methods to calculate relative solubilities	5
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	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
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders	4
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights	4
Turbo prediction: a new approach for bioactivity prediction	4
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	4
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	4
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	4
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective	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
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	4
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins	4
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	4
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	4
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations	4
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	4
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	4
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy	4
Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods	3
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	3
Multitarget-directed ligands in Alzheimer’s disease: identification of AChE and BACE1 inhibitors by in silico approaches	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
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	3
Calibrating the gap: a user-friendly aqueous $$\text{p}K_a$$ prediction protocol for organic acids, alcohols, and amines	3
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	3
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	3
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	3
Thermodynamic free energy map for the non-oxidative glycolysis pathways	3
μOR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification	3
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	3
Quantum algorithm for protein-ligand docking sites identification in the interaction space	3
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	3
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy	3
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation	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
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	2
Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma	2
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	2
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	2
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	2
Medt5-bi: bidirectional translation between drug indications and molecular structures using a chemically-aware transformer	2
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	2
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability	2
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
On the force field optimisation of $$\beta$$-lactam cores using the force field Toolkit	2
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium	2
Is there a common allosteric binding site for G-protein coupled receptors?	2
Design, synthesis, and integrated in silico analysis of novel difluoroboron curcumin analogues as potent inhibitors of the K562 leukemia cell line	2
HCV genotyping and rational computational designing of an immunogenic multiepitope vaccine against genotype 3a	2
Prospects for the structure‒function evolution of SARS-CoV-2 main protease inhibitors	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
OPTUNA optimization for predicting chemical respiratory toxicity using ML models	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
ADis-QSAR: a machine learning model based on biological activity differences of compounds	2
Convolidine as potent BACE1 inhibitor for Alzheimer’s disease; in-silico coupled with in-vitro assessment	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: Exploring DrugCentral: from molecular structures to clinical effects	2
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	2
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	2
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	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
Deep learning model for activity cliffs prediction: a comprehensive approach to protein kinase inhibitors	2
Novel insight into CFTR gene’s single nucleotide variants classification via in-silico analysis of a conserved site	1
Anticancer potential of novel benzothiazolyl piperidine-3-carboxamide derivatives as CDKs and VEGFR2 multi-target kinase inhibitors	1
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface	1
Structure-guided discovery of microtubule affinity-regulating kinase 4 inhibitory potential of Harmane: towards therapeutic targeting of Alzheimer’s disease	1
Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding	1
On the relevance of query definition in the performance of 3D ligand-based virtual screening	1
Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation	1
Computational characterization and machine learning analysis of quantum optimized marine fungal metabolites targeting PD-L1 in cancer immunotherapy	1
ChemFlow_py: a flexible toolkit for docking and rescoring	1
Rethinking the applicability domain analysis in QSAR models	1
Comparison study of dominant molecular sequence representation based on diffusion model	1
Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays	1
Molecular simulations of paclitaxel binding to mutant β-tubulin: insights into chemotherapy resistance	1

Molecular structure, DFT computations, and docking studies of an imidazo[1,2-a]pyridine derivative containing 1,2,3-triazole and 4-bromophenyl moieties	1
Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment	1
Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products	1
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey	1
DeepTargetClass: a web-based platform for predicting protein target classes of small molecules	1
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis	1
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	1
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity	1
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics	1
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA	1
Computational investigation to identify multi-targeted anti-hyperglycemic potential of substituted 2-Mercaptobenzimidazole derivatives and synthesis of new α-glucosidase inhibitors	1
Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules	1
Fungal metabolite Ochratoxin A inhibits MrkD1P of multidrug-resistant Klebsiella pneumoniae: Integrated computational and in vitro validation	1
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations	1
pKa prediction for small molecules: an overview of experimental, quantum, and machine learning-based approaches	1
Molecular dynamics simulations as a guide for modulating small molecule aggregation	1
MiR-146/TNF-α/IL-6/osteocalcin crosstalk in anti-rheumatic potential of Galleria mellonella hemolymph from computational molecular modeling to in-vivo validation	1
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat	1
AI-powered IC50 prediction for p53 inhibitors drug-target interaction via hybrid graph neural networks	1
Targeting multiple pathways with virtual screening to identify the multi-target agent for Alzheimer’s disease treatment	1
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	1
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	1
Molecular dynamics modeling and spectroscopic property prediction of V-type nerve agents for safe handling	1
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	1
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	1
Computational QSAR study of novel 2-aminothiazol-4(5H)-one derivatives as 11β‐HSD1 inhibitors	1
In silico discovery and experimental validation of natural derivatives as inhibitor of phosphoinositide Kinase, PIKfyve	1
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	1