Molecular Informatics

Article	Citations
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Cover Picture: (Mol. Inf. 6/2021)	41
Cover Picture: (Mol. Inf. 2/2025)	35
MAYA (Multiple ActivitY Analyzer): An Open Access Tool to Explore Structure‐Multiple Activity Relationships in the Chemical Universe	34
Cover Picture: (Mol. Inf. 1/2022)	32
Cover Picture: (Mol. Inf. 2/2022)	30
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Cover Picture: (Mol. Inf. 8/2022)	18
Cover Picture: (Mol. Inf. 10/2024)	17
Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches**	17
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS‐CoV‐2 Main Protease	17
Cover Picture: (Mol. Inf. 1/2023)	17
Active learning approaches in molecule pKi prediction	16
Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers	16
The freedom space – a new set of commercially available molecules for hit discovery	16
In Silicoprediction of inhibitors for multiple transporters via machine learning methods	14
Prediction of adverse drug reactions due to genetic predisposition using deep neural networks	14
Cover Picture: (Mol. Inf. 9/2024)	14
Prediction of blood‐brain barrier permeability using machine learning approaches based on various molecular representation	13

Fragment‐based deep molecular generation using hierarchical chemical graph representation and multi‐resolution graph variational autoencoder	13
Augmenting bioactivity by docking‐generated multiple ligand poses to enhance machine learning and pharmacophore modelling: discovery of new TTK inhibitors as case study	12
Computer‐aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones	12
Application of Molecular Docking, Homology Modeling, and Chemometric Approaches to Neonicotinoid Toxicity against Aphis craccivora	11
Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies	11
Highly Accurate Filters to Flag Frequent Hitters in AlphaScreen Assays by Suggesting their Mechanism	11
Chemical Reactivity Prediction: Current Methods and Different Application Areas	11
A Dataset of Computational Reaction Barriers for the Claisen Rearrangement: Chemical and Numerical Analysis	10
Structural Fractal Analysis of the Active Site of Acetylcholinesterase in Complexes with Huperzine A, Galantamine, and Donepezil	10
Block‐wise Exploration of Molecular Descriptors with Multi‐block Orthogonal Component Analysis (MOCA)	10
Identification of a PD1/PD‐L1 inhibitor by structure‐based pharmacophore modelling, virtual screening, molecular docking and biological evaluation**	9
LCP: Simple Representation of Docking Poses for Machine Learning: A Case Study on Xanthine Oxidase Inhibitors	9
Gas‐to‐ionic liquid partition: QSPR modeling and mechanistic interpretation	9
A new set of KNIME nodes implementing the QPhAR algorithm	9
RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design	8
Ensemble docking based virtual screening of SARS‐CoV‐2 main protease inhibitors	8
An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis**	8
Development and Evaluation of Peptidomimetic Compounds against SARS‐CoV‐2 Spike Protein: An in silico and in vitro Study	8
FetoML: Interpretable predictions of the fetotoxicity of drugs based on machine learning approaches	8
A Descriptor Set for Quantitative Structure‐property Relationship Prediction in Biologics	7
A community effort in SARS‐CoV‐2 drug discovery	7
Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES‐1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor	7
MGRNN: Structure Generation of Molecules Based on Graph Recurrent Neural Networks	6
The Relevance of Goodness‐of‐fit, Robustness and Prediction Validation Categories of OECD‐QSAR Principles with Respect to Sample Size and Model Type	6
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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	6
Comparing Explanations of Molecular Machine Learning Models Generated with Different Methods for the Calculation of Shapley Values	6
Cover Picture: (Mol. Inf. 12/2021)	6
Cover Picture: (Mol. Inf. 3/2022)	6
GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit	6
Machine Learning in Drug Development for Neurological Diseases: A Review of Blood Brain Barrier Permeability Prediction Models	6
Cover Picture: (Mol. Inf. 8‐9/2023)	6
Cover Picture: (Mol. Inf. 1/2024)	5
PredictingS. aureusantimicrobial resistance with interpretable genomic space maps	5
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Similarity searching for anticandidal agents employing a repurposing approach	5
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Cover Picture: (Mol. Inf. 7/2021)	5
Discovery of natural‐derived Mpro inhibitors as therapeutic candidates for COVID‐19: Structure‐based pharmacophore screening combined with QSAR analysis	5
Pharmacophore‐guided Virtual Screening to Identify New β3‐adrenergic Receptor Agonists	4
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA	4
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Cover Picture: (Mol. Inf. 11/2024)	4
Cover Picture: (Mol. Inf. 3/2023)	4
Cell‐penetrating peptides predictors: A comparative analysis of methods and datasets	4
Predicting the duration of action of β2‐adrenergic receptor agonists: Ligand and structure‐based approaches	4

The Chemical Space Spanned by Manually Curated Datasets of Natural and Synthetic Compounds with Activities against SARS‐CoV‐2	4
Virtual screening of natural products to enhance melanogenosis	4
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Discovery of a Novel Antimicrobial Agent by the Virtual Screening of a Library of Small Molecules	4
Exploring data‐driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties	4
My 50 Years with Chemoinformatics	4
Cover Picture: (Mol. Inf. 12/2024)	3
Structure‐based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural‐product‐derived IRAK‐4 Inhibitors	3
Best of both worlds: An expansion of the state of the art pKa model with data from three industrial partners	3
Improving Molecular Design with Direct Inverse Analysis of QSAR/QSPR Model	3
Machine Learning Boosted Docking (HASTEN): An Open‐source Tool To Accelerate Structure‐based Virtual Screening Campaigns	3
Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation	3
Chemoinformatics and Machine Learning Approaches for Identifying Antiviral Compounds	3
ADMET Predictability at Boehringer Ingelheim: State‐of‐the‐Art, and Do Bigger Datasets or Algorithms Make a Difference?	3
Prediction of the Chemical Context for Buchwald‐Hartwig Coupling Reactions	3
Identification of 1,2,4‐Triazolylthioethanone Scaffold for the Design of New Acetylcholinesterase Inhibitors	3
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Review of the 8th autumn school in chemoinformatics	3
Editorial: Chemical Reactions Mining	2
Ultra‐Large Virtual Screening: Definition, Recent Advances, and Challenges in Drug Design	2
Cover Picture: (Mol. Inf. 11/2021)	2
Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure‐function insights	2
Kinematic analysis of kinases and their oncogenic mutations – Kinases and their mutation kinematic analysis	2
An AI‐based Prediction Model for Drug‐drug Interactions in Osteoporosis and Paget's Diseases from SMILES	2
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	2
Design, Bio‐evaluation and Molecular Dynamics Simulation of Novel GSK‐3β Inhibitors	2
Identification of Trovafloxacin, Ozanimod, and Ozenoxacin as Potent c‐Myc G‐Quadruplex Stabilizers to Suppress c‐Myc Transcription and Myeloma Growth	2
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library	2
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An Attempt to Classify Elementary Reactions on the Basis of TS Motifs	2
Turbo Similarity Searching: Effect of Partial Ranking and Fusion Rules on ChEMBL Database	2
De novo drug design based on patient gene expression profiles via deep learning	2
Exploring cooperative molecular contacts using a PostgreSQL database system	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
Technique of Augmenting Molecular Graph Data by Perturbating Hidden Features	2
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Cover Picture: (4/2021)	2
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	2
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Co‐model for chemical toxicity prediction based on multi‐task deep learning	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
Network‐Based Approaches for Drug Repositioning	2
NP Navigator: A New Look at the Natural Product Chemical Space	1
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MolPredictX: Online Biological Activity Predictions by Machine Learning Models	1
An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values	1
AliNA – a deep learning program for RNA secondary structure prediction	1
Cover Picture: (Mol. Inf. 4/2023)	1
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm	1
Developing a Generative Model Utilizing Self‐attention Networks: Application to Materials/Drug Discovery	1
Cover Picture: (Mol. Inf. 6/2022)	1
Cover Picture: (Mol. Inf. 11/2022)	1
Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra‐large virtual screening	1
Artificial neural network models driven novel virtual screening workflow for the identification and biological evaluation of BACE1 inhibitors	1
Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance	1
Protein Binding Site Representation in Latent Space	1
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Translating from Proteins to Ribonucleic Acids for Ligand‐binding Site Detection	1
Generative Adversarial Networks for De Novo Molecular Design	1
Cover Picture: (Mol. Inf. 5/2024)	1
Feature importance‐based interpretation of UMAP‐visualized polymer space	1
In silico construction of a focused fragment library facilitating exploration of chemical space**	1
Chemoinformatics for corrosion science: Data‐driven modeling of corrosion inhibition by organic molecules	1
Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization	1
Extended Activity Cliffs‐Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions	1
Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction	1
PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening	1
Cover Picture: (Mol. Inf. 8/2024)	0
A machine learning strategy with clustering under sampling of majority instances for predicting drug target interactions**	0
Differential Consistency Analysis: Which Similarity Measures can be Applied in Drug Discovery?	0
A machine learning q‐RASPR approach for efficient predictions of the specific surface area of perovskites**	0
Metabolovigilance: Associating Drug Metabolites with Adverse Drug Reactions	0
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Predicting the Price of Molecules Using Their Predicted Synthetic Pathways**	0
Computational Designing and Prediction of ADMET Properties of Four Novel Imidazole‐based Drug Candidates Inhibiting Heme Oxygenase‐1 Causing Cancers	0
CIPSI: An open chemical intellectual property service for medicinal chemists	0
Computer‐aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study	0
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MFPS_CNN: Multi‐filter Pattern Scanning from Position‐specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters	0
Chemical language models for molecular design	0
Conjugated quantitative structure‐property relationship models: Prediction of kinetic characteristics linked by the Arrhenius equation	0
Structural and Dynamic Assessment of Disease‐Causing Mutations for the Carnitine Transporter OCTN2	0
Cover Picture: (Mol. Inf. 7/2024)	0
Discovery of New HER2 Inhibitors via Computational Docking, Pharmacophore Modeling, and Machine Learning	0
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Data‐driven approaches for identifying hyperparameters in multi‐step retrosynthesis	0
Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction	0
Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical Spaces	0
Natural‐Language Processing (NLP) based feature extraction technique in Deep‐Learning model to predict the Blood‐Brain‐Barrier permeability of molecules	0
Kinetic solubility: Experimental and machine‐learning modeling perspectives	0
CoLiNN: A Tool for Fast Chemical Space Visualization of Combinatorial Libraries Without Enumeration	0
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A Scaffold‐based Deep Generative Model Considering Molecular Stereochemical Information	0
Advances in Computational Polypharmacology	0
Machine Learning to Predict Homolytic Dissociation Energies of C−H Bonds: Calibration of DFT‐based Models with Experimental Data	0
Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints	0
Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen	0
Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation**	0
Quasi‐supervised Strategies for Compound‐protein Interaction Prediction	0
The VEGA web service: multipurpose online tools for molecular modelling and docking analyses	0
Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies	0
Critical Assessment of State‐of‐the‐Art Ligand‐Based Virtual Screening Methods	0
French dispatch: GTM‐based analysis of the Chimiothèque Nationale Chemical Space	0
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Cover Picture: (Mol. Inf. 7/2022)	0
Exploration of the Chemical Space of DNA‐encoded Libraries	0
Inhibitor Assessment against the LpxC Enzyme of Antibiotic‐resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays	0
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ACE2‐Variants Indicate Potential SARS‐CoV‐2‐Susceptibility in Animals: A Molecular Dynamics Study	0
A Molecular Representation to Identify Isofunctional Molecules	0
ET‐score: Improving Protein‐ligand Binding Affinity Prediction Based on Distance‐weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm	0
Pathway‐based prediction of the therapeutic effects and mode of action of custom‐made multiherbal medicines	0
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GB‐score: Minimally designed machine learning scoring function based on distance‐weighted interatomic contact features	0
Cover Picture: (Mol. Inf. 8/2021)	0
DIGEP‐Pred 2.0: A web application for predicting drug‐induced cell signaling and gene expression changes	0
Prediction of the Appropriate Temperature and Pressure for Polymer Dissolution Using Machine Learning Models	0
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Exploring activity landscapes with extended similarity: is Tanimoto enough?	0
In silico Studies on the Interaction between Mpro and PLpro From SARS‐CoV‐2 and Ebselen, its Metabolites and Derivatives	0
Cover Picture: (Mol. Inf. 7/2023)	0
The macrocycle inhibitor landscape of SLC‐transporter	0
Phenothiazine‐based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi	0
A comparison between 2D and 3D descriptors in QSAR modeling based on bio‐active conformations	0
Cover Picture: (Mol. Inf. 11/2023)	0
Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin‐microtubule System	0
Comparing search algorithms on the retrosynthesis problem	0
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QSPR Modelling of the Solubility of Drug and Drug‐like Compounds in Supercritical Carbon Dioxide	0
Cover Picture: (Mol. Inf. 12/2022)	0
GCLmf: A Novel Molecular Graph Contrastive Learning Framework Based on Hard Negatives and Application in Toxicity Prediction**	0
Drug Repurposing for Newly Emerged Diseases via Network‐based Inference on a Gene‐disease‐drug Network	0
Virtual Screening Inhibitors of Ubiquitin‐specific Protease 7 Combining Pharmacophore Modeling and Molecular Docking	0
FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening	0
Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post‐processing	0
Accelerating Molecular Docking using Machine Learning Methods	0
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	0
Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation	0
New Pharmacophore Fingerprints and Weight‐matrix Learning for Virtual Screening. Application to Bcr‐Abl Data	0
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Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host‐pathogen Interaction Network Parameters	0
Classification of tastants: A deep learning based approach	0
New QSPRs for Liquid Heat Capacity	0
Cover Picture: (Mol. Inf. 12/2023)	0
Updating and profiling the natural product‐likeness of Latin American compound libraries**	0
Reaction Data Curation I: Chemical Structures and Transformations Standardization	0
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Chemoinformatic Analysis of Isothiocyanates: Their Impact in Nature and Medicine	0
Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization	0
Cover Picture: (Mol. Inf. 10/2022)	0
ERL‐ProLiGraph: Enhanced representation learning on protein‐ligand graph structured data for binding affinity prediction	0
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Cover Picture: (Mol. Inf. 2/2024)	0
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Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina	0
DeepBBBP: High Accuracy Blood‐brain‐barrier Permeability Prediction with a Mixed Deep Learning Model	0
Cover Picture: (Mol. Inf. 6/2024)	0
BIOMX‐DB: A web application for the BIOFACQUIM natural product database	0
Cover Picture: (Mol. Inf. 3/2025)	0
Cover Picture: (Mol. Inf. 10/2021)	0
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	0
Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors**	0
Development of novel ligands against SARS‐CoV‐2 Mpro enzyme: an in silico and in vitro Study	0
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NMSDR: Drug repurposing approach based on transcriptome data and network module similarity	0
Molecular Odor Prediction Using Olfactory Receptor Information	0
Sulfotransferase‐mediated phase II drug metabolism prediction of substrates and sites using accessibility and reactivity‐based algorithms	0
Identifying Chirality in Line Drawings of Molecules Using Imbalanced Dataset Sampler for a Multilabel Classification Task	0
Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets	0
Chemical Multiverse: An Expanded View of Chemical Space	0
Multi‐targeted Drug Repurposing Approach for Breast Cancer via Integrated Functional Network Analysis	0