Journal of Cheminformatics

Article	Citations
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	357
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	198
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	93
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	78
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	72
Transformer-based molecular optimization beyond matched molecular pairs	69
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	58
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	51
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	50
Deep learning of multimodal networks with topological regularization for drug repositioning	50
Paths to cheminformatics: Q&A with Ann M. Richard	50
VSFlow: an open-source ligand-based virtual screening tool	50
Explainable uncertainty quantifications for deep learning-based molecular property prediction	50
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	49
One chiral fingerprint to find them all	47
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	47
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	45
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	45
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	44
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	42
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	41
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	40
Bitter peptide prediction using graph neural networks	39
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	39
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	38

Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	38
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	38
PyL3dMD: Python LAMMPS 3D molecular descriptors package	37
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	37
Splitting chemical structure data sets for federated privacy-preserving machine learning	37
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	35
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	35
canSAR chemistry registration and standardization pipeline	35
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	33
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	33
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	32
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	32
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	31
A systematic review of deep learning chemical language models in recent era	30
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	28
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	28
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	27
Diversifying cheminformatics	27
New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application	26
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	26
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	25
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	25
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	24
VGSC-DB: an online database of voltage-gated sodium channels	24
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds	23
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	23
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices	23
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)	22
The specification game: rethinking the evaluation of drug response prediction for precision oncology	21
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	21
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	21
Implementation of a soft grading system for chemistry in a Moodle plugin	21
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	21
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	21
Reaction rebalancing: a novel approach to curating reaction databases	21
Automatic molecular fragmentation by evolutionary optimisation	21
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty	20
Application of deep metric learning to molecular graph similarity	20
A machine learning platform for the discovery of materials	20
Chemical reaction network knowledge graphs: the OntoRXN ontology	20
Activity cliff-aware reinforcement learning for de novo drug design	19
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	19
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	19
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	19
Visualising lead optimisation series using reduced graphs	19
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	19
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	19
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	19
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	19
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	19

TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	18
Deepmol: an automated machine and deep learning framework for computational chemistry	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	18
Ensemble completeness in conformer sampling: the case of small macrocycles	18
Learning protein-ligand binding affinity with atomic environment vectors	18
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	18
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	17
Searching chemical databases in the pre-history of cheminformatics	17
piscesCSM: prediction of anticancer synergistic drug combinations	17
TB-IECS: an accurate machine learning-based scoring function for virtual screening	17
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	17
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	16
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	16
Integrating synthetic accessibility with AI-based generative drug design	16
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	16
UnCorrupt SMILES: a novel approach to de novo design	16
MolNexTR: a generalized deep learning model for molecular image recognition	16
The effect of noise on the predictive limit of QSAR models	15
Nonadditivity in public and inhouse data: implications for drug design	15
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	15
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	14
DECIMER—hand-drawn molecule images dataset	14
Human-in-the-loop active learning for goal-oriented molecule generation	14
What makes a reaction network “chemical”?	14
QPHAR: quantitative pharmacophore activity relationship: method and validation	14
Advancing material property prediction: using physics-informed machine learning models for viscosity	14
Decrypting orphan GPCR drug discovery via multitask learning	14
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	13
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	13
Automated molecular structure segmentation from documents using ChemSAM	13
ReMODE: a deep learning-based web server for target-specific drug design	13
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	13
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	12
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	12
SMILES all around: structure to SMILES conversion for transition metal complexes	12
IDSM ChemWebRDF: SPARQLing small-molecule datasets	12
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	12
Solvent flashcards: a visualisation tool for sustainable chemistry	12
OWSum: algorithmic odor prediction and insight into structure-odor relationships	12
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	12
PIKAChU: a Python-based informatics kit for analysing chemical units	12
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models	12
How can SHAP values help to shape metabolic stability of chemical compounds?	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	12
Application of machine reading comprehension techniques for named entity recognition in materials science	12
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	12
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	11
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	11
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning	11
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	11
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	11
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling	11
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors	11
kMoL: an open-source machine and federated learning library for drug discovery	11
Building shape-focused pharmacophore models for effective docking screening	10
Deep scaffold hopping with multimodal transformer neural networks	10
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties	10
PUResNet: prediction of protein-ligand binding sites using deep residual neural network	10
Large language models open new way of AI-assisted molecule design for chemists	10
Correction: Reconstruction of lossless molecular representations from fingerprints	10
Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors	10
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data	10
E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays	10
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling	10
Integrating QSAR modelling with reinforcement learning for Syk inhibitor discovery	10
HobPre: accurate prediction of human oral bioavailability for small molecules	10
InflamNat: web-based database and predictor of anti-inflammatory natural products	10
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	9
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	9
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	9
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design	9
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability	9
Relative molecule self-attention transformer	9
Processing binding data using an open-source workflow	9
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	9
A molecule perturbation software library and its application to study the effects of molecular design constraints	9
COMA: efficient structure-constrained molecular generation using contractive and margin losses	9

A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles	8
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates	8
Classification of battery compounds using structure-free Mendeleev encodings	8
FAIR chemical structures in the Journal of Cheminformatics	8
Barlow Twins deep neural network for advanced 1D drug–target interaction prediction	8
StreaMD: the toolkit for high-throughput molecular dynamics simulations	8
Improving VAE based molecular representations for compound property prediction	8
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations	8
Double-head transformer neural network for molecular property prediction	8
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	8
PubChem synonym filtering process using crowdsourcing	8
Matched pairs demonstrate robustness against inter-assay variability	8
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study	8
Combatting over-specialization bias in growing chemical databases	8
Explaining and avoiding failure modes in goal-directed generation of small molecules	7
Reproducible MS/MS library cleaning pipeline in matchms	7
Unveiling polyphenol-protein interactions: a comprehensive computational analysis	7
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	7
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	7
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data	7
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation	7
QSPR modeling of selectivity at infinite dilution of ionic liquids	7
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	7
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB	7
Improving the performance of models for one-step retrosynthesis through re-ranking	7
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	7
Exploring QSAR models for activity-cliff prediction	7
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	7
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	7
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry	6
Deep learning integration of molecular and interactome data for protein–compound interaction prediction	6
hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses	6
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions	6
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	6
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization	6
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	6
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis	6
Charged aerosol detector response modeling for fatty acids based on experimental settings and molecular features: a machine learning approach	6
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model	6
Evaluating the generalizability of graph neural networks for predicting collision cross section	6
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	6
Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture	6
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	6
“DompeKeys”: a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases	6
Investigation of the structure-odor relationship using a Transformer model	6
Positional embeddings and zero-shot learning using BERT for molecular-property prediction	6
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling	6
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	6
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package	6
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	6
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	5
Context-dependent similarity analysis of analogue series for structure–activity relationship transfer based on a concept from natural language processing	5
Accelerating the inference of string generation-based chemical reaction models for industrial applications	5
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	5
Art driven by visual representations of chemical space	5
A new workflow for the effective curation of membrane permeability data from open ADME information	5
Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator	5
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data	5
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop	5
Identifying uncertainty in physical–chemical property estimation with IFSQSAR	5
A look back at a pilot of the citation typing ontology	5
DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data	5
Development of a chemogenomics library for phenotypic screening	5
Efficient virtual high-content screening using a distance-aware transformer model	5
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	5
Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction	5
MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model	5
Molecular generation by Fast Assembly of (Deep)SMILES fragments	5
Development of machine learning classifiers to predict compound activity on prostate cancer cell lines	5
Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning	5
Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability	5
Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models	4
MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle	4
InertDB as a generative AI-expanded resource of biologically inactive small molecules from PubChem	4
Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence	4
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons	4
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis	4
Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence	4
DrugTax: package for drug taxonomy identification and explainable feature extraction	4
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)	4
Biomedical data analyses facilitated by open cheminformatics workflows	4
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules	4
LigninGraphs: lignin structure determination with multiscale graph modeling	4
Correction: Global reactivity models are impactful in industrial synthesis applications	4
Reply to “FAIR chemical structure in the Journal of Cheminformatics”	4
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES	4
ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction	4
Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model	4
Predicting protein network topology clusters from chemical structure using deep learning	4
Comparative evaluation of methods for the prediction of protein–ligand binding sites	4
A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence	4
Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow	4