Molecular Informatics

Article	Citations
Cover Picture: (Mol. Inf. 6/2021)	74
Cover Picture: (Mol. Inf. 1/2023)	44
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS‐CoV‐2 Main Protease	39
Cover Picture: (Mol. Inf. 4/2022)	35
Chemical Reactivity Prediction: Current Methods and Different Application Areas	32
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Application of Molecular Docking, Homology Modeling, and Chemometric Approaches to Neonicotinoid Toxicity against Aphis craccivora	30
Development and Evaluation of Peptidomimetic Compounds against SARS‐CoV‐2 Spike Protein: An in silico and in vitro Study	29
Fragment‐based deep molecular generation using hierarchical chemical graph representation and multi‐resolution graph variational autoencoder	26
A Descriptor Set for Quantitative Structure‐property Relationship Prediction in Biologics	22
Cover Picture: (Mol. Inf. 1/2024)	20
A community effort in SARS‐CoV‐2 drug discovery	20
Review of the 8th autumn school in chemoinformatics	19
Technique of Augmenting Molecular Graph Data by Perturbating Hidden Features	18
Predicting the duration of action of β2‐adrenergic receptor agonists: Ligand and structure‐based approaches	18
Machine Learning Boosted Docking (HASTEN): An Open‐source Tool To Accelerate Structure‐based Virtual Screening Campaigns	18
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	17
Identification of Trovafloxacin, Ozanimod, and Ozenoxacin as Potent c‐Myc G‐Quadruplex Stabilizers to Suppress c‐Myc Transcription and Myeloma Growth	17
Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure‐function insights	16
Virtual screening of natural products to enhance melanogenosis	16
Structure‐based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural‐product‐derived IRAK‐4 Inhibitors	16
Kinematic analysis of kinases and their oncogenic mutations – Kinases and their mutation kinematic analysis	15
Predicting the bandgap and efficiency of perovskite solar cells using machine learning methods	14
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Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation	14

Cover Picture: (Mol. Inf. 6/2022)	13
Cover Picture: (Mol. Inf. 5/2024)	13
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Chemoinformatic Analysis of Isothiocyanates: Their Impact in Nature and Medicine	11
Natural‐Language Processing (NLP) based feature extraction technique in Deep‐Learning model to predict the Blood‐Brain‐Barrier permeability of molecules	11
Use of tree‐based machine learning methods to screen affinitive peptides based on docking data	11
Cover Picture: (Mol. Inf. 11/2023)	11
Cover Picture: (Mol. Inf. 7/2024)	10
Data‐driven approaches for identifying hyperparameters in multi‐step retrosynthesis	10
Cover Picture: (Mol. Inf. 6/2024)	10
Antibacterial Activity Prediction of Plant Secondary Metabolites Based on a Combined Approach of Graph Clustering and Deep Neural Network	9
Cover Picture: (Mol. Inf. 4/2025)	9
Multi‐Task ADME/PK prediction at industrial scale: leveraging large and diverse experimental datasets**	9
Cover Picture: (Mol. Inf. 9/2021)	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: (5/2021)	8
The VEGA web service: multipurpose online tools for molecular modelling and docking analyses	8
KNIME Workflows for Chemoinformatic Characterization of Chemical Databases	8
In silico Studies on the Interaction between Mpro and PLpro From SARS‐CoV‐2 and Ebselen, its Metabolites and Derivatives	8
Computational Designing and Prediction of ADMET Properties of Four Novel Imidazole‐based Drug Candidates Inhibiting Heme Oxygenase‐1 Causing Cancers	8
Cover Picture: (Mol. Inf. 10/2022)	7
A comparison between 2D and 3D descriptors in QSAR modeling based on bio‐active conformations	7
Cover Picture: (Mol. Inf. 12/2023)	7
Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation**	7
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BIOMX‐DB: A web application for the BIOFACQUIM natural product database	6
A Scaffold‐based Deep Generative Model Considering Molecular Stereochemical Information	6
Cover Picture: (Mol. Inf. 1/2022)	6
Cover Picture: (Mol. Inf. 7/2023)	6
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Cover Picture: (Mol. Inf. 10/2024)	6
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Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host‐pathogen Interaction Network Parameters	6
Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies	6
Identification of a PD1/PD‐L1 inhibitor by structure‐based pharmacophore modelling, virtual screening, molecular docking and biological evaluation**	5
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My 50 Years with Chemoinformatics	5
Machine Learning in Drug Development for Neurological Diseases: A Review of Blood Brain Barrier Permeability Prediction Models	5
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PredictingS. aureusantimicrobial resistance with interpretable genomic space maps	5
Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches**	5
Cover Picture: (Mol. Inf. 8‐9/2023)	5
Network‐Based Approaches for Drug Repositioning	5
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AliNA – a deep learning program for RNA secondary structure prediction	4
Feature importance‐based interpretation of UMAP‐visualized polymer space	4
GDMol: Generative Double‐Masking Self‐Supervised Learning for Molecular Property Prediction	4

Turbo Similarity Searching: Effect of Partial Ranking and Fusion Rules on ChEMBL Database	4
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Generative Adversarial Networks for De Novo Molecular Design	4
A Molecular Representation to Identify Isofunctional Molecules	4
Exploring activity landscapes with extended similarity: is Tanimoto enough?	3
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The macrocycle inhibitor landscape of SLC‐transporter	3
Cover Picture: (Mol. Inf. 5/2022)	3
Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post‐processing	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
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Targeting of essential mycobacterial replication enzyme DnaG primase revealed Mitoxantrone and Vapreotide as novel mycobacterial growth inhibitors**	3
Molecular Energies Derived from Deep Learning: Application to the Prediction of Formation Enthalpies Up to High Energy Compounds	3
Modeling Carbon Basicity	3
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Quasi‐supervised Strategies for Compound‐protein Interaction Prediction	3
Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen	3
Cover Picture: (Mol. Inf. 5/2023)	3
Chemoinformatic regression methods and their applicability domain	3
Cover Picture: (Mol. Inf. 2/2023)	3
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
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Extended Activity Cliffs‐Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions	2
NP Navigator: A New Look at the Natural Product Chemical Space	2
Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation	2
The Chemical Space Spanned by Manually Curated Datasets of Natural and Synthetic Compounds with Activities against SARS‐CoV‐2	2
QSPR Modelling of the Solubility of Drug and Drug‐like Compounds in Supercritical Carbon Dioxide	2
An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis**	2
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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
Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra‐large virtual screening	2
Cover Picture: (Mol. Inf. 11/2021)	2
Prediction of the Chemical Context for Buchwald‐Hartwig Coupling Reactions	2
Cover Picture: (Mol. Inf. 7/2021)	2
Cell‐penetrating peptides predictors: A comparative analysis of methods and datasets	2
MAYA (Multiple ActivitY Analyzer): An Open Access Tool to Explore Structure‐Multiple Activity Relationships in the Chemical Universe	2
A machine learning strategy with clustering under sampling of majority instances for predicting drug target interactions**	2
Identification of 1,2,4‐Triazolylthioethanone Scaffold for the Design of New Acetylcholinesterase Inhibitors	2
Protein Binding Site Representation in Latent Space	2
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm	2
Ultra‐Large Virtual Screening: Definition, Recent Advances, and Challenges in Drug Design	2
PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening	2
Cover Picture: (Mol. Inf. 12/2021)	2
GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit	2
Computer‐aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones	2
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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
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
Drug Repurposing for Newly Emerged Diseases via Network‐based Inference on a Gene‐disease‐drug Network	1
ET‐score: Improving Protein‐ligand Binding Affinity Prediction Based on Distance‐weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm	1
In silico prediction of drug‐induced liver injury with a complementary integration strategy based on hybrid representation	1
Cover Picture: (Mol. Inf. 6/2023)	1
Navigating pharmacophore space to identify activity discontinuities: A case study with BCR‐ABL	1
Chemography‐guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst	1
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Kinetic solubility: Experimental and machine‐learning modeling perspectives	1
Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets	1
Discovery of Potent and Isoform‐selective Histone Deacetylase Inhibitors Using Structure‐based Virtual Screening and Biological Evaluation	1
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Molecular Odor Prediction Using Olfactory Receptor Information	1
Entropy‐based lamarckian quantum‐behaved particle swarm optimization for flexible ligand docking	1
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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
Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors**	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
Towards an Enrichment Optimization Algorithm (EOA)‐based Target Specific Docking Functions for Virtual Screening	1
Design, Bio‐evaluation and Molecular Dynamics Simulation of Novel GSK‐3β Inhibitors	0
Discovery of New HER2 Inhibitors via Computational Docking, Pharmacophore Modeling, and Machine Learning	0
A Topology‐Enhanced Multi‐Viewed Contrastive Approach for Molecular Graph Representation Learning and Classification	0
Co‐model for chemical toxicity prediction based on multi‐task deep learning	0
Updating and profiling the natural product‐likeness of Latin American compound libraries**	0
Overlap of On‐demand Ultra‐large Combinatorial Spaces with On‐the‐shelf Drug‐like Libraries	0
Sulfotransferase‐mediated phase II drug metabolism prediction of substrates and sites using accessibility and reactivity‐based algorithms	0
Cover Picture: (Mol. Inf. 3/2024)	0
Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization	0
Pathway‐based prediction of the therapeutic effects and mode of action of custom‐made multiherbal medicines	0

Advances in Computational Polypharmacology	0
Cover Picture: (Mol. Inf. 1/2025)	0
Cover Picture: (Mol. Inf. 4/2024)	0
Prediction of adverse drug reactions due to genetic predisposition using deep neural networks	0
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Prediction of Reaction Yield for Buchwald‐Hartwig Cross‐coupling Reactions Using Deep Learning	0
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CoLiNN: A Tool for Fast Chemical Space Visualization of Combinatorial Libraries Without Enumeration	0
Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies	0
An Integrated Fuzzy Neural Network and Topological Data Analysis for Molecular Graph Representation Learning and Property Forecasting	0
Structural and Dynamic Assessment of Disease‐Causing Mutations for the Carnitine Transporter OCTN2	0
Gas‐to‐ionic liquid partition: QSPR modeling and mechanistic interpretation	0
Developing a Generative Model Utilizing Self‐attention Networks: Application to Materials/Drug Discovery	0
In silico construction of a focused fragment library facilitating exploration of chemical space**	0
Exploring data‐driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties	0
Highly Accurate Filters to Flag Frequent Hitters in AlphaScreen Assays by Suggesting their Mechanism	0
An Attempt to Classify Elementary Reactions on the Basis of TS Motifs	0
ERL‐ProLiGraph: Enhanced representation learning on protein‐ligand graph structured data for binding affinity prediction	0
Accelerating Molecular Docking using Machine Learning Methods	0
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Predicting the Price of Molecules Using Their Predicted Synthetic Pathways**	0
Compression of molecular fingerprints with autoencoder networks	0
Simple User‐Friendly Reaction Format	0
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Cover Picture: (Mol. Inf. 8/2024)	0
MFPS_CNN: Multi‐filter Pattern Scanning from Position‐specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters	0
Improving Molecular Design with Direct Inverse Analysis of QSAR/QSPR Model	0
Cover Picture: (Mol. Inf. 7/2022)	0
DIGEP‐Pred 2.0: A web application for predicting drug‐induced cell signaling and gene expression changes	0
Editorial: Chemical Reactions Mining	0
Chemical language models for molecular design	0
Discovery of natural‐derived Mpro inhibitors as therapeutic candidates for COVID‐19: Structure‐based pharmacophore screening combined with QSAR analysis	0
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NMSDR: Drug repurposing approach based on transcriptome data and network module similarity	0
Cover Picture: (Mol. Inf. 9/2022)	0
New QSPRs for Liquid Heat Capacity	0
DeepBBBP: High Accuracy Blood‐brain‐barrier Permeability Prediction with a Mixed Deep Learning Model	0
Discovery of Inhibitors for Mycobacterium Tuberculosis Peptide Deformylase Based on Virtual Screening in Silico	0
Cover Picture: (Mol. Inf. 4/2023)	0
Cover Picture: (Mol. Inf. 2/2022)	0
MGRNN: Structure Generation of Molecules Based on Graph Recurrent Neural Networks	0
Cover Picture: (Mol. Inf. 10/2021)	0
Virtual Screening Inhibitors of Ubiquitin‐specific Protease 7 Combining Pharmacophore Modeling and Molecular Docking	0
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A Dataset of Computational Reaction Barriers for the Claisen Rearrangement: Chemical and Numerical Analysis	0
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Absorption matters: A closer look at popular oral bioavailability rules for drug approvals	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
Cover Picture: (Mol. Inf. 11/2022)	0
Multi‐targeted Drug Repurposing Approach for Breast Cancer via Integrated Functional Network Analysis	0
Multiple Conformer Descriptors for QSAR Modeling	0
Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina	0
An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values	0
Deep Modeling of Gain‐of‐Function Mutations on Androgen Receptor	0
RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design	0
Artificial neural network models driven novel virtual screening workflow for the identification and biological evaluation of BACE1 inhibitors	0
Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance	0
Cover Picture: (Mol. Inf. 10/2023)	0
Inhibitor Assessment against the LpxC Enzyme of Antibiotic‐resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays	0
Exploring cooperative molecular contacts using a PostgreSQL database system	0
Cover Picture: (Mol. Inf. 8/2021)	0
Cover Picture: (Mol. Inf. 12/2022)	0
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GCLmf: A Novel Molecular Graph Contrastive Learning Framework Based on Hard Negatives and Application in Toxicity Prediction**	0
Development of novel ligands against SARS‐CoV‐2 Mpro enzyme: an in silico and in vitro Study	0
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA	0
Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints	0
Exploration of the Chemical Space of DNA‐encoded Libraries	0
French dispatch: GTM‐based analysis of the Chimiothèque Nationale Chemical Space	0
Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS‐CoV‐2: A Combinedin silicoandin vitroStudy	0
Classification of tastants: A deep learning based approach	0
Computer‐aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study	0
Active learning approaches in molecule pKi prediction	0
Similarity searching for anticandidal agents employing a repurposing approach	0
Reaction Data Curation I: Chemical Structures and Transformations Standardization	0
Machine Learning to Predict Homolytic Dissociation Energies of C−H Bonds: Calibration of DFT‐based Models with Experimental Data	0
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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
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Metabolovigilance: Associating Drug Metabolites with Adverse Drug Reactions	0
Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical Spaces	0
LCP: Simple Representation of Docking Poses for Machine Learning: A Case Study on Xanthine Oxidase Inhibitors	0
MolPredictX: Online Biological Activity Predictions by Machine Learning Models	0
Cover Picture: (Mol. Inf. 3/2023)	0
A new set of KNIME nodes implementing the QPhAR algorithm	0
Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction	0
Structural Insight on the Selectivity of Calyx[4]Arene‐Based Inhibitors of Mg2+−Dependent Atp‐Hydrolases	0
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Chemical Multiverse: An Expanded View of Chemical Space	0
Chemoinformatics for corrosion science: Data‐driven modeling of corrosion inhibition by organic molecules	0
Translating from Proteins to Ribonucleic Acids for Ligand‐binding Site Detection	0
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Comparing search algorithms on the retrosynthesis problem	0
FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening	0