Molecular Informatics

Article	Citations
An AI‐based Prediction Model for Drug‐drug Interactions in Osteoporosis and Paget's Diseases from SMILES	62
In silico Studies on the Interaction between Mpro and PLpro From SARS‐CoV‐2 and Ebselen, its Metabolites and Derivatives	34
ADMET Predictability at Boehringer Ingelheim: State‐of‐the‐Art, and Do Bigger Datasets or Algorithms Make a Difference?	26
Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies	26
Chemical Multiverse: An Expanded View of Chemical Space	26
Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina	24
In Silico Targeting Human Multidrug Transporter ABCG2 in Breast Cancer: Database Screening, Molecular Docking, and Molecular Dynamics Study	21
HDAC3i‐Finder: A Machine Learning‐based Computational Tool to Screen for HDAC3 Inhibitors	21
A machine learning q‐RASPR approach for efficient predictions of the specific surface area of perovskites**	20
Differential Consistency Analysis: Which Similarity Measures can be Applied in Drug Discovery?	19
Reaction Data Curation I: Chemical Structures and Transformations Standardization	19
A Descriptor Set for Quantitative Structure‐property Relationship Prediction in Biologics	17
Targeting Mycobacterium Tuberculosis Enoyl‐Acyl Carrier Protein Reductase Using Computational Tools for Identification of Potential Inhibitor and their Biological Activity	16
Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets	16
Embedding of Molecular Structure Using Molecular Hypergraph Variational Autoencoder with Metric Learning	15
Targeting SARS‐CoV‐2 Spike Protein/ACE2 Protein‐Protein Interactions: a Computational Study	14
NP Navigator: A New Look at the Natural Product Chemical Space	14
Generative Adversarial Networks for De Novo Molecular Design	14
Benchmarking Accuracy and Generalizability of Four Graph Neural Networks Using Large In Vitro ADME Datasets from Different Chemical Spaces	13
Multi‐targeted Drug Repurposing Approach for Breast Cancer via Integrated Functional Network Analysis	13
Chemoinformatics and Machine Learning Approaches for Identifying Antiviral Compounds	13
DeepBBBP: High Accuracy Blood‐brain‐barrier Permeability Prediction with a Mixed Deep Learning Model	12
Prediction of Reaction Yield for Buchwald‐Hartwig Cross‐coupling Reactions Using Deep Learning	11
Exploration of the Chemical Space of DNA‐encoded Libraries	11
QSPR Modelling of the Solubility of Drug and Drug‐like Compounds in Supercritical Carbon Dioxide	11

ChemBoost: A Chemical Language Based Approach for Protein – Ligand Binding Affinity Prediction	10
The Relevance of Goodness‐of‐fit, Robustness and Prediction Validation Categories of OECD‐QSAR Principles with Respect to Sample Size and Model Type	10
ET‐score: Improving Protein‐ligand Binding Affinity Prediction Based on Distance‐weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm	10
Using Active Learning to Develop Machine Learning Models for Reaction Yield Prediction	9
Machine Learning Boosted Docking (HASTEN): An Open‐source Tool To Accelerate Structure‐based Virtual Screening Campaigns	9
Multiple Conformer Descriptors for QSAR Modeling	9
Chemical Reactivity Prediction: Current Methods and Different Application Areas	9
Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host‐pathogen Interaction Network Parameters	9
Network‐Based Approaches for Drug Repositioning	9
Exploring activity landscapes with extended similarity: is Tanimoto enough?	8
Locally Optimizable Joint Embedding Framework to Design Nitrogen‐rich Molecules that are Similar but Improved	8
A comparison between 2D and 3D descriptors in QSAR modeling based on bio‐active conformations	8
Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS‐CoV‐2: A Combinedin silicoandin vitroStudy	7
RENATE: A Pseudo‐retrosynthetic Tool for Synthetically Accessible de novo Design	7
Advances in Computational Polypharmacology	7
Overlap of On‐demand Ultra‐large Combinatorial Spaces with On‐the‐shelf Drug‐like Libraries	7
An Integrative in silico Drug Repurposing Approach for Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease	7
HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra‐large chemical libraries	7
MolPredictX: Online Biological Activity Predictions by Machine Learning Models	7
MGRNN: Structure Generation of Molecules Based on Graph Recurrent Neural Networks	6
Exploring the Gallic and Cinnamic Acids Chimeric Derivatives as Anticancer Agents over HeLa Cell Line: An in silico and in vitro Study	6
Pharmacophore‐guided Virtual Screening to Identify New β3‐adrenergic Receptor Agonists	6
MFPS_CNN: Multi‐filter Pattern Scanning from Position‐specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters	6
Virtual Screening Inhibitors of Ubiquitin‐specific Protease 7 Combining Pharmacophore Modeling and Molecular Docking	5
Ligand‐based Discovery of Novel Small Molecule Inhibitors of RON Receptor Tyrosine Kinase	5
PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening	5
MetaPASS: A Web Application for Analyzing the Biological Activity Spectrum of Organic Compounds Taking into Account their Biotransformation	5
Computational Designing and Prediction of ADMET Properties of Four Novel Imidazole‐based Drug Candidates Inhibiting Heme Oxygenase‐1 Causing Cancers	5
Translating from Proteins to Ribonucleic Acids for Ligand‐binding Site Detection	5
Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation	5
Identification of a PD1/PD‐L1 inhibitor by structure‐based pharmacophore modelling, virtual screening, molecular docking and biological evaluation**	5
Critical Assessment of State‐of‐the‐Art Ligand‐Based Virtual Screening Methods	5
New QSPRs for Liquid Heat Capacity	5
Machine Learning Methods to Predict the Terrestrial and Marine Origin of Natural Products	5
Pharmacophore Modeling of Targets Infested with Activity CliffsviaMolecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study	5
Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies	4
Drug Repurposing for Newly Emerged Diseases via Network‐based Inference on a Gene‐disease‐drug Network	4
Molecular Energies Derived from Deep Learning: Application to the Prediction of Formation Enthalpies Up to High Energy Compounds	4
Discovery of Potent and Isoform‐selective Histone Deacetylase Inhibitors Using Structure‐based Virtual Screening and Biological Evaluation	4
Identification of Trovafloxacin, Ozanimod, and Ozenoxacin as Potent c‐Myc G‐Quadruplex Stabilizers to Suppress c‐Myc Transcription and Myeloma Growth	4
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	4
Inhibitor Assessment against the LpxC Enzyme of Antibiotic‐resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays	4
Chemical language models for molecular design	4
Effect of Learning Dataset for Identification of Active Molecules: A Case Study of Integrin αIIbβ3 Inhibitors	4
Prediction of the Chemical Context for Buchwald‐Hartwig Coupling Reactions	4
Peptidomimetics in Silico	4
Discovery of Inhibitors for Mycobacterium Tuberculosis Peptide Deformylase Based on Virtual Screening in Silico	4
Data‐driven approaches for identifying hyperparameters in multi‐step retrosynthesis	4
De novo drug design based on patient gene expression profiles via deep learning	4
Augmenting bioactivity by docking‐generated multiple ligand poses to enhance machine learning and pharmacophore modelling: discovery of new TTK inhibitors as case study	3

Computer‐aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study	3
Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints	3
Chemoinformatic Analysis of Isothiocyanates: Their Impact in Nature and Medicine	3
AliNA – a deep learning program for RNA secondary structure prediction	3
Chemoinformatics for the Safety of Energetic and Reactive Materials at Ineris	3
Visualization and Analysis of the REACH‐chemical Space with Generative Topographic Mapping	3
ACE2‐Variants Indicate Potential SARS‐CoV‐2‐Susceptibility in Animals: A Molecular Dynamics Study	3
Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post‐processing	3
Absorption matters: A closer look at popular oral bioavailability rules for drug approvals	3
Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance	3
Discovery of natural‐derived Mpro inhibitors as therapeutic candidates for COVID‐19: Structure‐based pharmacophore screening combined with QSAR analysis	3
Block‐wise Exploration of Molecular Descriptors with Multi‐block Orthogonal Component Analysis (MOCA)	3
Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin‐microtubule System	3
GB‐score: Minimally designed machine learning scoring function based on distance‐weighted interatomic contact features	3
Machine Learning to Predict Homolytic Dissociation Energies of C−H Bonds: Calibration of DFT‐based Models with Experimental Data	3
Prediction of the Partition Coefficient between Adipose Tissue and Blood for Environmental Chemicals: From Single QSAR Models to an Integrated Approach	3
Feature importance‐based interpretation of UMAP‐visualized polymer space	3
Computer‐aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones	2
A Dataset of Computational Reaction Barriers for the Claisen Rearrangement: Chemical and Numerical Analysis	2
Antibacterial Activity Prediction of Plant Secondary Metabolites Based on a Combined Approach of Graph Clustering and Deep Neural Network	2
Classification of tastants: A deep learning based approach	2
Artificial neural network models driven novel virtual screening workflow for the identification and biological evaluation of BACE1 inhibitors	2
Design, Bio‐evaluation and Molecular Dynamics Simulation of Novel GSK‐3β Inhibitors	2
A community effort in SARS‐CoV‐2 drug discovery	2
Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS‐CoV‐2 Main Protease	2
Highly Accurate Filters to Flag Frequent Hitters in AlphaScreen Assays by Suggesting their Mechanism	2
Comparing search algorithms on the retrosynthesis problem	2
Compression of molecular fingerprints with autoencoder networks	2
Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction	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
Co‐model for chemical toxicity prediction based on multi‐task deep learning	2
LCP: Simple Representation of Docking Poses for Machine Learning: A Case Study on Xanthine Oxidase Inhibitors	2
Structural Fractal Analysis of the Active Site of Acetylcholinesterase in Complexes with Huperzine A, Galantamine, and Donepezil	2
Quasi‐supervised Strategies for Compound‐protein Interaction Prediction	2
Improvement of the Structure Generator DAECS with Respect to Structural Diversity	2
Predicting the bandgap and efficiency of perovskite solar cells using machine learning methods	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
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	2
In silico prediction of drug‐induced liver injury with a complementary integration strategy based on hybrid representation	1
Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization	1
Predicting the duration of action of β2‐adrenergic receptor agonists: Ligand and structure‐based approaches	1
Structure‐based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural‐product‐derived IRAK‐4 Inhibitors	1
Development and Evaluation of Peptidomimetic Compounds against SARS‐CoV‐2 Spike Protein: An in silico and in vitro Study	1
An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis**	1
Metabolovigilance: Associating Drug Metabolites with Adverse Drug Reactions	1
Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors**	1
Updating and profiling the natural product‐likeness of Latin American compound libraries**	1
Development of novel ligands against SARS‐CoV‐2 Mpro enzyme: an in silico and in vitro Study	1
Developing a Generative Model Utilizing Self‐attention Networks: Application to Materials/Drug Discovery	1
Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra‐large virtual screening	1
Exploring data‐driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties	1
Technique of Augmenting Molecular Graph Data by Perturbating Hidden Features	1
Application of Molecular Docking, Homology Modeling, and Chemometric Approaches to Neonicotinoid Toxicity against Aphis craccivora	1
FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening	1
NMSDR: Drug repurposing approach based on transcriptome data and network module similarity	1
Conjugated quantitative structure‐property relationship models: Prediction of kinetic characteristics linked by the Arrhenius equation	1
French dispatch: GTM‐based analysis of the Chimiothèque Nationale Chemical Space	1
Entropy‐based lamarckian quantum‐behaved particle swarm optimization for flexible ligand docking	1
An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values	1
Ambit‐SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation	1
Discovery of a Novel Antimicrobial Agent by the Virtual Screening of a Library of Small Molecules	1
Fragment‐based deep molecular generation using hierarchical chemical graph representation and multi‐resolution graph variational autoencoder	1
GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit	1
Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen	1
Phenothiazine‐based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi	1
New Pharmacophore Fingerprints and Weight‐matrix Learning for Virtual Screening. Application to Bcr‐Abl Data	1
The macrocycle inhibitor landscape of SLC‐transporter	1
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Prediction of adverse drug reactions due to genetic predisposition using deep neural networks	0
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Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library	0
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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

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Gas‐to‐ionic liquid partition: QSPR modeling and mechanistic interpretation	0
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Virtual screening of natural products to enhance melanogenosis	0
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Cell‐penetrating peptides predictors: A comparative analysis of methods and datasets	0
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Targeting of essential mycobacterial replication enzyme DnaG primase revealed Mitoxantrone and Vapreotide as novel mycobacterial growth inhibitors**	0
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Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches**	0
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm	0
Identification of 1,2,4‐Triazolylthioethanone Scaffold for the Design of New Acetylcholinesterase Inhibitors	0
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Prediction of blood‐brain barrier permeability using machine learning approaches based on various molecular representation	0
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ERL‐ProLiGraph: Enhanced representation learning on protein‐ligand graph structured data for binding affinity prediction	0
The freedom space – a new set of commercially available molecules for hit discovery	0
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Chemoinformatic regression methods and their applicability domain	0
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Natural‐Language Processing (NLP) based feature extraction technique in Deep‐Learning model to predict the Blood‐Brain‐Barrier permeability of molecules	0
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Active learning approaches in molecule pKi prediction	0
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Review of the 8th autumn school in chemoinformatics	0
DIGEP‐Pred 2.0: A web application for predicting drug‐induced cell signaling and gene expression changes	0
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Predicting S. aureus antimicrobial resistance with interpretable genomic space maps	0
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA	0
My 50 Years with Chemoinformatics	0
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In silico construction of a focused fragment library facilitating exploration of chemical space**	0
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Kinematic analysis of kinases and their oncogenic mutations – Kinases and their mutation kinematic analysis	0
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Multi‐Task ADME/PK prediction at industrial scale: leveraging large and diverse experimental datasets**	0
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Navigating pharmacophore space to identify activity discontinuities: A case study with BCR‐ABL	0
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Similarity searching for anticandidal agents employing a repurposing approach	0
Use of tree‐based machine learning methods to screen affinitive peptides based on docking data	0
In Silico prediction of inhibitors for multiple transporters via machine learning methods	0
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Cheminformatics Analysis of Fluoroquinolones and their Inhibition Potency Against Four Pathogens	0
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Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES‐1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor	0
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A new set of KNIME nodes implementing the QPhAR algorithm	0
Turbo Similarity Searching: Effect of Partial Ranking and Fusion Rules on ChEMBL Database	0
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Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure‐function insights	0
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Exploring cooperative molecular contacts using a PostgreSQL database system	0
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Best of both worlds: An expansion of the state of the art pKa model with data from three industrial partners	0
Towards an Enrichment Optimization Algorithm (EOA)‐based Target Specific Docking Functions for Virtual Screening	0
Editorial: Chemical Reactions Mining	0
FetoML: Interpretable predictions of the fetotoxicity of drugs based on machine learning approaches	0
Chemoinformatics for corrosion science: Data‐driven modeling of corrosion inhibition by organic molecules	0
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Navigating a 1E+60 Chemical Space of Peptide/Peptoid Oligomers	0
GDMol: Generative Double‐Masking Self‐Supervised Learning for Molecular Property Prediction	0
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Ensemble docking based virtual screening of SARS‐CoV‐2 main protease inhibitors	0
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