Molecular Informatics

Article	Citations
	66
Cover Picture: (Mol. Inf. 1/2023)	62
Fragment‐based deep molecular generation using hierarchical chemical graph representation and multi‐resolution graph variational autoencoder	54
A community effort in SARS‐CoV‐2 drug discovery	47
Current Insights on Skin Permeability Data and Quantitative Structure‐Property Relationship Modeling	37
Review of the 8th autumn school in chemoinformatics	34
Cover Picture: (Mol. Inf. 1/2024)	31
Virtual screening of natural products to enhance melanogenosis	30
Predicting the duration of action of β2‐adrenergic receptor agonists: Ligand and structure‐based approaches	26
Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure‐function insights	25
Application of automated machine learning in the identification of multi‐target‐directed ligands blocking PDE4B, PDE8A, and TRPA1 with potential use in the treatment of asthma and COPD	23
LapGAT: A Semi‐Supervised Learning Framework for Drug–Target Interaction Prediction	23
Cover Picture: (Mol. Inf. 5/2024)	21
Drug Search and Design Considering Cell Specificity of Chemically Induced Gene Expression Profiles for Disease‐Associated Tissues	21
Cover Picture: (Mol. Inf. 6/2022)	17
Kinematic analysis of kinases and their oncogenic mutations – Kinases and their mutation kinematic analysis	17
	16
	15
	15
Predicting the bandgap and efficiency of perovskite solar cells using machine learning methods	15
Neural Network Models for Prediction of Biological Activity using Molecular Dynamics Data: A Case of Photoswitchable Peptides	14
Cover Picture: (Mol. Inf. 7/2024)	14
Cover Picture: (Mol. Inf. 6/2024)	12
Cover Picture: (Mol. Inf. 4/2025)	12
Natural‐Language Processing (NLP) based feature extraction technique in Deep‐Learning model to predict the Blood‐Brain‐Barrier permeability of molecules	11

Rapid Assessment of Virtually Synthesizable Chemical Structures via Support Vector Machine Models	11
Data‐driven approaches for identifying hyperparameters in multi‐step retrosynthesis	11
Cover Picture: (Mol. Inf. 11/2023)	11
Use of tree‐based machine learning methods to screen affinitive peptides based on docking data	11
Discovery of a pocket network on the domain 5 of the TrkB receptor – A potential new target in the quest for the new ligands	10
The VEGA web service: multipurpose online tools for molecular modelling and docking analyses	10
Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation**	10
Multi‐Task ADME/PK prediction at industrial scale: leveraging large and diverse experimental datasets**	10
A comparison between 2D and 3D descriptors in QSAR modeling based on bio‐active conformations	9
LiProS: Findable, Accessible, Interoperable, and Reusable Data Simulation Workflow to Predict Accurate Lipophilicity Profiles for Small Molecules	9
Cover Picture: (Mol. Inf. 7/2025)	9
Structure–Activity Relationships and Design of Focused Libraries Tailored for Staphylococcus Aureus Inhibition	9
	9
KNIME Workflows for Chemoinformatic Characterization of Chemical Databases	9
Cover Picture: (Mol. Inf. 12/2023)	8
	8
Cover Picture: (Mol. Inf. 7/2023)	8
	8
Cover Picture: (Mol. Inf. 10/2022)	8
BIOMX‐DB: A web application for the BIOFACQUIM natural product database	7
Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches**	7
In Silico Identification of Novel and Potent Inhibitors Against Mutant BRAF (V600E), MD Simulations, Free Energy Calculations, and Experimental Determination of Binding Affinity	7
Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies	7
Read‐Across Structure‐Property Relationship‐Based Superior Prediction of Fraction Unbound in Plasma from Chemical Structure: Interpretable Models with Minimum Descriptors	7
A Scaffold‐based Deep Generative Model Considering Molecular Stereochemical Information	7
Cover Picture: (Mol. Inf. 10/2024)	7
Identification of a PD1/PD‐L1 inhibitor by structure‐based pharmacophore modelling, virtual screening, molecular docking and biological evaluation**	7
Predicting S. aureus antimicrobial resistance with interpretable genomic space maps	6
My 50 Years with Chemoinformatics	6
Spherical GTM: A New Proposition for Visualization of Chemical Data	6
	6
	6
	6
	6
Machine Learning Models Predicting Solubility and Polymerizability of Polyimides Considering Multiple Monomers for CO 2 Separation Membranes	6
Machine Learning in Drug Development for Neurological Diseases: A Review of Blood Brain Barrier Permeability Prediction Models	6
	6
Cover Picture: (Mol. Inf. 8‐9/2023)	6
	6
Cover Picture: (Mol. Inf. 5/2023)	5
A Molecular Representation to Identify Isofunctional Molecules	5
The macrocycle inhibitor landscape of SLC‐transporter	5
Cover Picture: (Mol. Inf. 10/2025)	5
GDMol: Generative Double‐Masking Self‐Supervised Learning for Molecular Property Prediction	5
AliNA – a deep learning program for RNA secondary structure prediction	5
Feature importance‐based interpretation of UMAP‐visualized polymer space	5
Network Analysis of the Organic Chemistry in Patents, Literature, and Pharmaceutical Industry	4
11 th National Conference of the French Chemoinformatics Society (SFCi)	4
Chemoinformatic regression methods and their applicability domain	4
Enhancing the Reliability of Integrated Consensus Strategies to Boost Docking‐Based Screening Campaigns Using Publicly Available Docking Programs	4

Cover Picture: (Mol. Inf. 5/2022)	4
Modeling Carbon Basicity	4
Therapeutic Potential of Amyloid‐β Interactors in Rapidly Progressive Alzheimer's Disease—An In Silico Study	4
Cover Picture: (Mol. Inf. 5‐6/2025)	4
Targeting of essential mycobacterial replication enzyme DnaG primase revealed Mitoxantrone and Vapreotide as novel mycobacterial growth inhibitors**	4
Exploring activity landscapes with extended similarity: is Tanimoto enough?	4
Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin‐microtubule System	3
Identifying Chirality in Line Drawings of Molecules Using Imbalanced Dataset Sampler for a Multilabel Classification Task	3
	3
Finding Pathways in Reaction Networks Guided by Energy Barriers Using Integer Linear Programing	3
Integrated workflow for the identification of new GABAAR positive allosteric modulators based on the in silico screening with further in vitro validation. Case study using Ena	3
Computer‐aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones	3
Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post‐processing	3
	3
Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen	3
Cover Picture: (Mol. Inf. 8/2025)	3
Cover Picture: (Mol. Inf. 2/2023)	3
A machine learning strategy with clustering under sampling of majority instances for predicting drug target interactions**	3
A Multistep Computational Approach to Achieve a Complete Human 5‐Lipoxygenase Structure and Provide a Pharmacophore Model for Further Drug Design	2
Development of Machine Learning‐Based Models for Mutagenicity Predictions with Applications to Non‐Sugar Sweeteners	2
	2
	2
GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit	2
The Chemical Space Spanned by Manually Curated Datasets of Natural and Synthetic Compounds with Activities against SARS‐CoV‐2	2
Protein Binding Site Representation in Latent Space	2
	2
	2
An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis**	2
Cell‐penetrating peptides predictors: A comparative analysis of methods and datasets	2
Ligand B‐Factor Index: A Metric for Prioritizing Protein‐Ligand Complexes in Docking	2
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm	2
Pharmacophore Modeling of Targets Infested with Activity CliffsviaMolecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study	2
Ultra‐Large Virtual Screening: Definition, Recent Advances, and Challenges in Drug Design	2
MAYA (Multiple ActivitY Analyzer): An Open Access Tool to Explore Structure‐Multiple Activity Relationships in the Chemical Universe	2
Interpretable and Scalable Similarity Metrics for DNA‐Encoded Library Design Using Generative Topographic Mapping	2
Navigating pharmacophore space to identify activity discontinuities: A case study with BCR‐ABL	1
In silico prediction of drug‐induced liver injury with a complementary integration strategy based on hybrid representation	1
Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra‐large virtual screening	1
	1
Foundation and Multimodal Models for Drug Discovery in Molecular Informatics: Principles, Evaluation, and Practical Guidance	1
Chemography‐guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst	1
	1
Exploring the Gallic and Cinnamic Acids Chimeric Derivatives as Anticancer Agents over HeLa Cell Line: An in silico and in vitro Study	1
The Use of DeepQSAR Models for the Discovery of Peptides With Enhanced Antimicrobial and Antibiofilm Potential	1
Extended Activity Cliffs‐Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions	1
Entropy‐based lamarckian quantum‐behaved particle swarm optimization for flexible ligand docking	1
MetaStab‐Analyzer: Classification and Regression Models for Metabolic Stability Prediction	1
	1
	1
Cover Picture: (Mol. Inf. 6/2023)	1
Molecular Odor Prediction Using Olfactory Receptor Information	1
HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra‐large chemical libraries	1
From High Dimensions to Human Insight: Exploring Dimensionality Reduction for Chemical Space Visualization	1
Cover Picture: (Mol. Inf. 11‐12/2025)	1
	1
Towards an Enrichment Optimization Algorithm (EOA)‐based Target Specific Docking Functions for Virtual Screening	1
Cover Picture: (Mol. Inf. 3/2025)	0
Transformer Learning in Sequence‐Based Drug Design Depends on Compound Memorization and Similarity of Sequence‐Compound Pairs	0
Machine Learning to Predict Homolytic Dissociation Energies of C−H Bonds: Calibration of DFT‐based Models with Experimental Data	0
Translating from Proteins to Ribonucleic Acids for Ligand‐binding Site Detection	0
Kinetic solubility: Experimental and machine‐learning modeling perspectives	0
	0
	0
In silico construction of a focused fragment library facilitating exploration of chemical space**	0
	0
	0
Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction	0
DIGEP‐Pred 2.0: A web application for predicting drug‐induced cell signaling and gene expression changes	0
Gas‐to‐ionic liquid partition: QSPR modeling and mechanistic interpretation	0
An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values	0
Cover Picture: (Mol. Inf. 3/2024)	0
Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES‐1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor	0
Cover Picture: (Mol. Inf. 1/2025)	0
Structural Insight on the Selectivity of Calyx[4]Arene‐Based Inhibitors of Mg2+−Dependent Atp‐Hydrolases	0
Interpret Gaussian Process Models by Using Integrated Gradients	0
	0
NMSDR: Drug repurposing approach based on transcriptome data and network module similarity	0
Cover Picture: (Mol. Inf. 2/2024)	0
Machine Learning‐Based Identification of Petroleum Distillates and Gasoline Traces Using Measured and Synthetic GC Spectra from Collected Samples	0
Pathway‐based prediction of the therapeutic effects and mode of action of custom‐made multiherbal medicines	0

	0
CIPSI: An open chemical intellectual property service for medicinal chemists	0
Comparing Explanations of Molecular Machine Learning Models Generated with Different Methods for the Calculation of Shapley Values	0
Sulfotransferase‐mediated phase II drug metabolism prediction of substrates and sites using accessibility and reactivity‐based algorithms	0
A new set of KNIME nodes implementing the QPhAR algorithm	0
Cover Picture: (Mol. Inf. 8/2022)	0
Exploring cooperative molecular contacts using a PostgreSQL database system	0
Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints	0
Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina	0
Cover Picture: (Mol. Inf. 9/2025)	0
Exploring data‐driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties	0
Discovery of New HER2 Inhibitors via Computational Docking, Pharmacophore Modeling, and Machine Learning	0
Discovery of natural‐derived Mpro inhibitors as therapeutic candidates for COVID‐19: Structure‐based pharmacophore screening combined with QSAR analysis	0
	0
	0
Cover Picture: (Mol. Inf. 10/2023)	0
Cover Picture: (Mol. Inf. 11/2024)	0
FetoML: Interpretable predictions of the fetotoxicity of drugs based on machine learning approaches	0
	0
Phenothiazine‐based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi	0
De novo drug design based on patient gene expression profiles via deep learning	0
Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization	0
CoLiNN: A Tool for Fast Chemical Space Visualization of Combinatorial Libraries Without Enumeration	0
Artificial neural network models driven novel virtual screening workflow for the identification and biological evaluation of BACE1 inhibitors	0
Development of novel ligands against SARS‐CoV‐2 Mpro enzyme: an in silico and in vitro Study	0
Cover Picture: (Mol. Inf. 9/2022)	0
An Integrated Fuzzy Neural Network and Topological Data Analysis for Molecular Graph Representation Learning and Property Forecasting	0
Overlap of On‐demand Ultra‐large Combinatorial Spaces with On‐the‐shelf Drug‐like Libraries	0
Ensemble docking based virtual screening of SARS‐CoV‐2 main protease inhibitors	0
	0
Inhibitor Assessment against the LpxC Enzyme of Antibiotic‐resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays	0
A machine learning q‐RASPR approach for efficient predictions of the specific surface area of perovskites**	0
Compression of molecular fingerprints with autoencoder networks	0
Simple User‐Friendly Reaction Format	0
Predicting the Price of Molecules Using Their Predicted Synthetic Pathways**	0
Prediction of adverse drug reactions due to genetic predisposition using deep neural networks	0
GCLmf: A Novel Molecular Graph Contrastive Learning Framework Based on Hard Negatives and Application in Toxicity Prediction**	0
Cover Picture: (Mol. Inf. 4/2023)	0
FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening	0
	0
In Silicoprediction of inhibitors for multiple transporters via machine learning methods	0
Cover Picture: (Mol. Inf. 4/2024)	0
Application of machine learning‐based read‐across structure‐property relationship (RASPR) as a new tool for predictive modelling: Prediction of power conversion efficiency (PCE) for selected classes o	0
Critical Assessment of State‐of‐the‐Art Ligand‐Based Virtual Screening Methods	0
	0
Statistics and Ontology of Published Small Molecule Ring Systems	0
Similarity searching for anticandidal agents employing a repurposing approach	0
Cover Picture: (Mol. Inf. 2/2025)	0
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA	0
Cover Picture: (Mol. Inf. 7/2022)	0
Structural and Dynamic Assessment of Disease‐Causing Mutations for the Carnitine Transporter OCTN2	0
The freedom space – a new set of commercially available molecules for hit discovery	0
Improving Molecular Design with Direct Inverse Analysis of QSAR/QSPR Model	0
Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction	0
Chemical Multiverse: An Expanded View of Chemical Space	0
Cover Picture: (Mol. Inf. 12/2024)	0
Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance	0
Cover Picture: (Mol. Inf. 11/2022)	0
Deep Modeling of Gain‐of‐Function Mutations on Androgen Receptor	0
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library	0
Exploration of (Ultra)Big Chemical Spaces	0
Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors**	0
An Attempt to Classify Elementary Reactions on the Basis of TS Motifs	0
Classification of tastants: A deep learning based approach	0
	0
MolPredictX: Online Biological Activity Predictions by Machine Learning Models	0
A Topology‐Enhanced Multi‐Viewed Contrastive Approach for Molecular Graph Representation Learning and Classification	0
Cover Picture: (Mol. Inf. 9/2024)	0
Chemoinformatics for corrosion science: Data‐driven modeling of corrosion inhibition by organic molecules	0
DeepMoDRP: A Multi‐Omics‐Based Deep Learning Framework for Drug Response Prediction in Brain Cancer	0
The Relevance of Goodness‐of‐fit, Robustness and Prediction Validation Categories of OECD‐QSAR Principles with Respect to Sample Size and Model Type	0
Infrared Spectral Descriptors for Reaction Yield Prediction: Toward Redefining Experimental Spaces	0
Cover Picture: (Mol. Inf. 12/2022)	0
Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization	0
Chemical language models for molecular design	0
A multi‐tier computational screening framework to effectively search the mutational space of SARS‐CoV‐2 receptor binding motif to identify mutants with enhanced ACE2 binding abilities	0
GB‐score: Minimally designed machine learning scoring function based on distance‐weighted interatomic contact features	0
Prediction of blood‐brain barrier permeability using machine learning approaches based on various molecular representation	0
French dispatch: GTM‐based analysis of the Chimiothèque Nationale Chemical Space	0
	0
	0
Active learning approaches in molecule pKi prediction	0
Updating and profiling the natural product‐likeness of Latin American compound libraries**	0
Augmenting bioactivity by docking‐generated multiple ligand poses to enhance machine learning and pharmacophore modelling: discovery of new TTK inhibitors as case study	0
Prediction of the Appropriate Temperature and Pressure for Polymer Dissolution Using Machine Learning Models	0
Cover Picture: (Mol. Inf. 3/2023)	0
Computer‐aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study	0
Accelerating Molecular Docking using Machine Learning Methods	0
	0
Update and ADMET Profile of the Latin American Natural Product Database: LANaPDB	0
Cover Picture: (Mol. Inf. 8/2024)	0
Advances in Computational Polypharmacology	0
Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers	0
Co‐model for chemical toxicity prediction based on multi‐task deep learning	0
Best of both worlds: An expansion of the state of the art pKa model with data from three industrial partners	0