Molecular Informatics

Article	Citations
	76
Application of Molecular Docking, Homology Modeling, and Chemometric Approaches to Neonicotinoid Toxicity against Aphis craccivora	48
Development and Evaluation of Peptidomimetic Compounds against SARS‐CoV‐2 Spike Protein: An in silico and in vitro Study	44
Fragment‐based deep molecular generation using hierarchical chemical graph representation and multi‐resolution graph variational autoencoder	43
A community effort in SARS‐CoV‐2 drug discovery	37
Cover Picture: (Mol. Inf. 4/2022)	36
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS‐CoV‐2 Main Protease	30
Chemical Reactivity Prediction: Current Methods and Different Application Areas	26
Cover Picture: (Mol. Inf. 1/2023)	26
A Descriptor Set for Quantitative Structure‐property Relationship Prediction in Biologics	25
Review of the 8th autumn school in chemoinformatics	25
Cover Picture: (Mol. Inf. 1/2024)	23
Virtual screening of natural products to enhance melanogenosis	22
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	22
Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure‐function insights	20
Predicting the duration of action of β2‐adrenergic receptor agonists: Ligand and structure‐based approaches	20
Structure‐based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural‐product‐derived IRAK‐4 Inhibitors	19
Technique of Augmenting Molecular Graph Data by Perturbating Hidden Features	18
Identification of Trovafloxacin, Ozanimod, and Ozenoxacin as Potent c‐Myc G‐Quadruplex Stabilizers to Suppress c‐Myc Transcription and Myeloma Growth	17
Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation	16
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Drug Search and Design Considering Cell Specificity of Chemically Induced Gene Expression Profiles for Disease‐Associated Tissues	15
Predicting the bandgap and efficiency of perovskite solar cells using machine learning methods	14
Cover Picture: (Mol. Inf. 5/2024)	14

Cover Picture: (Mol. Inf. 6/2022)	14
Kinematic analysis of kinases and their oncogenic mutations – Kinases and their mutation kinematic analysis	13
Use of tree‐based machine learning methods to screen affinitive peptides based on docking data	12
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Rapid Assessment of Virtually Synthesizable Chemical Structures via Support Vector Machine Models	12
Neural Network Models for Prediction of Biological Activity using Molecular Dynamics Data: A Case of Photoswitchable Peptides	12
Cover Picture: (Mol. Inf. 7/2024)	11
Multi‐Task ADME/PK prediction at industrial scale: leveraging large and diverse experimental datasets**	11
Cover Picture: (Mol. Inf. 4/2025)	11
Cover Picture: (Mol. Inf. 6/2024)	11
Natural‐Language Processing (NLP) based feature extraction technique in Deep‐Learning model to predict the Blood‐Brain‐Barrier permeability of molecules	10
Antibacterial Activity Prediction of Plant Secondary Metabolites Based on a Combined Approach of Graph Clustering and Deep Neural Network	10
Cover Picture: (Mol. Inf. 11/2023)	9
Cover Picture: (Mol. Inf. 9/2021)	9
Data‐driven approaches for identifying hyperparameters in multi‐step retrosynthesis	9
Chemoinformatic Analysis of Isothiocyanates: Their Impact in Nature and Medicine	9
A comparison between 2D and 3D descriptors in QSAR modeling based on bio‐active conformations	8
The VEGA web service: multipurpose online tools for molecular modelling and docking analyses	8
KNIME Workflows for Chemoinformatic Characterization of Chemical Databases	8
Discovery of a pocket network on the domain 5 of the TrkB receptor – A potential new target in the quest for the new ligands	8
Cover Picture: (Mol. Inf. 7/2025)	8
Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation**	8
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In Silico Identification of Novel and Potent Inhibitors Against Mutant BRAF (V600E), MD Simulations, Free Energy Calculations, and Experimental Determination of Binding Affinity	7
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Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies	7
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BIOMX‐DB: A web application for the BIOFACQUIM natural product database	7
Cover Picture: (Mol. Inf. 10/2024)	6
Cover Picture: (Mol. Inf. 1/2022)	6
Cover Picture: (Mol. Inf. 10/2022)	6
Machine Learning in Drug Development for Neurological Diseases: A Review of Blood Brain Barrier Permeability Prediction Models	6
Identification of a PD1/PD‐L1 inhibitor by structure‐based pharmacophore modelling, virtual screening, molecular docking and biological evaluation**	6
Cover Picture: (Mol. Inf. 12/2023)	6
A Scaffold‐based Deep Generative Model Considering Molecular Stereochemical Information	6
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Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches**	6
Cover Picture: (Mol. Inf. 7/2023)	6
Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host‐pathogen Interaction Network Parameters	6
Turbo Similarity Searching: Effect of Partial Ranking and Fusion Rules on ChEMBL Database	5
Cover Picture: (Mol. Inf. 8‐9/2023)	5
PredictingS. aureusantimicrobial resistance with interpretable genomic space maps	5
Spherical GTM: A New Proposition for Visualization of Chemical Data	5
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Network‐Based Approaches for Drug Repositioning	5
My 50 Years with Chemoinformatics	5
AliNA – a deep learning program for RNA secondary structure prediction	5
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A Molecular Representation to Identify Isofunctional Molecules	4

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Cover Picture: (Mol. Inf. 5/2022)	4
Modeling Carbon Basicity	4
Feature importance‐based interpretation of UMAP‐visualized polymer space	4
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Network Analysis of the Organic Chemistry in Patents, Literature, and Pharmaceutical Industry	4
Cover Picture: (Mol. Inf. 5/2023)	4
Cover Picture: (Mol. Inf. 5‐6/2025)	4
GDMol: Generative Double‐Masking Self‐Supervised Learning for Molecular Property Prediction	4
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The macrocycle inhibitor landscape of SLC‐transporter	4
Targeting of essential mycobacterial replication enzyme DnaG primase revealed Mitoxantrone and Vapreotide as novel mycobacterial growth inhibitors**	4
Molecular Energies Derived from Deep Learning: Application to the Prediction of Formation Enthalpies Up to High Energy Compounds	4
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Enhancing the Reliability of Integrated Consensus Strategies to Boost Docking‐Based Screening Campaigns Using Publicly Available Docking Programs	3
QSPR Modelling of the Solubility of Drug and Drug‐like Compounds in Supercritical Carbon Dioxide	3
Computer‐aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones	3
Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin‐microtubule System	3
MAYA (Multiple ActivitY Analyzer): An Open Access Tool to Explore Structure‐Multiple Activity Relationships in the Chemical Universe	3
Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen	3
Quasi‐supervised Strategies for Compound‐protein Interaction Prediction	3
Cover Picture: (Mol. Inf. 2/2023)	3
Chemoinformatic regression methods and their applicability domain	3
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Identifying Chirality in Line Drawings of Molecules Using Imbalanced Dataset Sampler for a Multilabel Classification Task	3
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GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit	3
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Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post‐processing	3
Exploring activity landscapes with extended similarity: is Tanimoto enough?	3
A machine learning strategy with clustering under sampling of majority instances for predicting drug target interactions**	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
Cover Picture: (Mol. Inf. 8/2025)	3
An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis**	3
HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra‐large chemical libraries	2
Entropy‐based lamarckian quantum‐behaved particle swarm optimization for flexible ligand docking	2
Ultra‐Large Virtual Screening: Definition, Recent Advances, and Challenges in Drug Design	2
Cell‐penetrating peptides predictors: A comparative analysis of methods and datasets	2
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Molecular Odor Prediction Using Olfactory Receptor Information	2
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm	2
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Navigating pharmacophore space to identify activity discontinuities: A case study with BCR‐ABL	2
Development of Machine Learning‐Based Models for Mutagenicity Predictions with Applications to Non‐Sugar Sweeteners	2
Cover Picture: (Mol. Inf. 12/2021)	2
Prediction of the Chemical Context for Buchwald‐Hartwig Coupling Reactions	2
Extended Activity Cliffs‐Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions	2
PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening	2
Protein Binding Site Representation in Latent Space	2
In silico prediction of drug‐induced liver injury with a complementary integration strategy based on hybrid representation	2
Cover Picture: (Mol. Inf. 6/2023)	2
The Chemical Space Spanned by Manually Curated Datasets of Natural and Synthetic Compounds with Activities against SARS‐CoV‐2	2
Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Na	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
Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation	2
Cover Picture: (Mol. Inf. 11/2021)	2
Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra‐large virtual screening	2
Cover Picture: (Mol. Inf. 2/2022)	1
FetoML: Interpretable predictions of the fetotoxicity of drugs based on machine learning approaches	1
In Silicoprediction of inhibitors for multiple transporters via machine learning methods	1
Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets	1
Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES‐1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor	1
Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors**	1
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From High Dimensions to Human Insight: Exploring Dimensionality Reduction for Chemical Space Visualization	1
Exploring the Gallic and Cinnamic Acids Chimeric Derivatives as Anticancer Agents over HeLa Cell Line: An in silico and in vitro Study	1
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Phenothiazine‐based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi	1
Cover Picture: (Mol. Inf. 9/2022)	1
Prediction of blood‐brain barrier permeability using machine learning approaches based on various molecular representation	1
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Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical Spaces	1
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Chemography‐guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst	1
Towards an Enrichment Optimization Algorithm (EOA)‐based Target Specific Docking Functions for Virtual Screening	1
Investigation of the Potential of Bile Acid Methyl Esters as Inhibitors of Aldo‐keto Reductase 1C2: Insight from Molecular Docking, Virtual Screening, Experimental Assays and Molecular Dynamics	1
Active learning approaches in molecule pKi prediction	1
Prediction of adverse drug reactions due to genetic predisposition using deep neural networks	1
Comparing Explanations of Molecular Machine Learning Models Generated with Different Methods for the Calculation of Shapley Values	1
Drug Repurposing for Newly Emerged Diseases via Network‐based Inference on a Gene‐disease‐drug Network	1

CoLiNN: A Tool for Fast Chemical Space Visualization of Combinatorial Libraries Without Enumeration	1
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Discovery of Potent and Isoform‐selective Histone Deacetylase Inhibitors Using Structure‐based Virtual Screening and Biological Evaluation	1
Kinetic solubility: Experimental and machine‐learning modeling perspectives	1