Journal of Cheminformatics

Article	Citations
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	115
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	109
Transformer-based molecular optimization beyond matched molecular pairs	73
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint	71
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	70
Explainable uncertainty quantifications for deep learning-based molecular property prediction	69
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	62
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	61
Assessing interaction recovery of predicted protein-ligand poses	58
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	58
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	56
Generating diversity and securing completeness in algorithmic retrosynthesis	52
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	52
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	49
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	48
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	47
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	46
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	46
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	44
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	42
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	42
Paths to cheminformatics: Q&A with Ann M. Richard	41
VSFlow: an open-source ligand-based virtual screening tool	40
One chiral fingerprint to find them all	39
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling	38

ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	38
Deep learning of multimodal networks with topological regularization for drug repositioning	37
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	34
MolPrice: assessing synthetic accessibility of molecules based on market value	34
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	34
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	33
Bitter peptide prediction using graph neural networks	33
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	32
Crossover operators for molecular graphs with an application to virtual drug screening	31
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	31
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	31
Shinyscreen: mass spectrometry data inspection and quality checking utility	31
Implementation of an open chemistry knowledge base with a Semantic Wiki	31
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	30
Splitting chemical structure data sets for federated privacy-preserving machine learning	30
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	30
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	29
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	29
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	28
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	28
Prediction model for chemical explosion consequences via multimodal feature fusion	28
The development of the generative adversarial supporting vector machine for molecular property generation	28
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	27
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	26
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	26
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	26
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	26
A systematic review of deep learning chemical language models in recent era	24
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	24
PyL3dMD: Python LAMMPS 3D molecular descriptors package	24
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	24
canSAR chemistry registration and standardization pipeline	24
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)	23
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	23
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	23
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	23
Diversifying cheminformatics	23
VGSC-DB: an online database of voltage-gated sodium channels	22
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	22
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices	22
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	22
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver	22
Reaction rebalancing: a novel approach to curating reaction databases	22
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	22
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	22
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	22
Automatic molecular fragmentation by evolutionary optimisation	21
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	21
Implementation of a soft grading system for chemistry in a Moodle plugin	21
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	21

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	21
Chemical reaction network knowledge graphs: the OntoRXN ontology	21
Visualising lead optimisation series using reduced graphs	20
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	20
Application of deep metric learning to molecular graph similarity	20
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach	20
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	18
Activity cliff-aware reinforcement learning for de novo drug design	18
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	18
Subgrapher: visual fingerprinting of chemical structures	18
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	18
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	18
The specification game: rethinking the evaluation of drug response prediction for precision oncology	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	17
A transformer based generative chemical language AI model for structural elucidation of organic compounds	17
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	17
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	17
Deepmol: an automated machine and deep learning framework for computational chemistry	16
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	16
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	16
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	16
Searching chemical databases in the pre-history of cheminformatics	16
TB-IECS: an accurate machine learning-based scoring function for virtual screening	15
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	15
Enhancing molecular property prediction with quantized GNN models	15
UnCorrupt SMILES: a novel approach to de novo design	15
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	15
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	15
piscesCSM: prediction of anticancer synergistic drug combinations	15
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	15
Integrating synthetic accessibility with AI-based generative drug design	15
Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability	15
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	15
MolNexTR: a generalized deep learning model for molecular image recognition	15
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement	14
VitroBert: modeling DILI by pretraining BERT on in vitro data	14
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	14
DECIMER—hand-drawn molecule images dataset	14
Human-in-the-loop active learning for goal-oriented molecule generation	13
Decrypting orphan GPCR drug discovery via multitask learning	13
What makes a reaction network “chemical”?	13
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	13
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	13
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	13
The effect of noise on the predictive limit of QSAR models	12
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
PIKAChU: a Python-based informatics kit for analysing chemical units	12
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	12
Application of machine reading comprehension techniques for named entity recognition in materials science	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
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	12
Advancing material property prediction: using physics-informed machine learning models for viscosity	12
Solvent flashcards: a visualisation tool for sustainable chemistry	12
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
Automated molecular structure segmentation from documents using ChemSAM	12
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	12
HobPre: accurate prediction of human oral bioavailability for small molecules	11
Correction: Reconstruction of lossless molecular representations from fingerprints	11
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	11
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling	11
ReMODE: a deep learning-based web server for target-specific drug design	11
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	11
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning	11
E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays	11
Integrating QSAR modelling with reinforcement learning for Syk inhibitor discovery	11
Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors	11
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models	11
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	11
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors	11
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	11
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	11
Evaluation of chirality descriptors derived from SMILES heteroencoders	11
Large language models open new way of AI-assisted molecule design for chemists	11
Deep scaffold hopping with multimodal transformer neural networks	11
kMoL: an open-source machine and federated learning library for drug discovery	11
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data	11
PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules	11
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	11

Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	11
OWSum: algorithmic odor prediction and insight into structure-odor relationships	11
Building shape-focused pharmacophore models for effective docking screening	11
Prediction of blood–brain barrier and Caco-2 permeability through the Enalos Cloud Platform: combining contrastive learning and atom-attention message passing neural networks	11
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	10
COMA: efficient structure-constrained molecular generation using contractive and margin losses	10
TraceMetrix: a traceable metabolomics interactive analysis platform	10
Advantages of two quantum programming platforms in quantum computing and quantum chemistry	10
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties	10
Machine learning-driven generation and screening of potential ionic liquids for cellulose dissolution	10
Benchmarking molecular conformer augmentation with context-enriched training: graph-based transformer versus GNN models	10
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability	10
Double-head transformer neural network for molecular property prediction	10
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	10
A molecule perturbation software library and its application to study the effects of molecular design constraints	10
Processing binding data using an open-source workflow	10
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	10
InflamNat: web-based database and predictor of anti-inflammatory natural products	10
Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching	10
Relative molecule self-attention transformer	9
PubChem synonym filtering process using crowdsourcing	9
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	9
Matched pairs demonstrate robustness against inter-assay variability	9
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design	9
Combatting over-specialization bias in growing chemical databases	9
StreaMD: the toolkit for high-throughput molecular dynamics simulations	9
Improving VAE based molecular representations for compound property prediction	8
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	8
Exploring QSAR models for activity-cliff prediction	8
Improving the performance of models for one-step retrosynthesis through re-ranking	8
Barlow Twins deep neural network for advanced 1D drug–target interaction prediction	8
Explaining and avoiding failure modes in goal-directed generation of small molecules	8
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	8
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data	8
Contrastive explanations for machine learning predictions in chemistry	8
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	8
Reproducible MS/MS library cleaning pipeline in matchms	8
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	7
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis	7
Classification of battery compounds using structure-free Mendeleev encodings	7
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB	7
QSPR modeling of selectivity at infinite dilution of ionic liquids	7
Application of the digital annealer unit in optimizing chemical reaction conditions for enhanced production yields	7
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model	7
Multi-fidelity graph neural networks for predicting toluene/water partition coefficients	7
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	7
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry	7
A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles	7
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates	7
Unveiling polyphenol-protein interactions: a comprehensive computational analysis	7
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	7
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization	7
Investigation of the structure-odor relationship using a Transformer model	7
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling	7
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	7
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	7
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations	7
xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides	7
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation	7
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package	7
Box embeddings for extending ontologies: a data-driven and interpretable approach	7
From molecules to data: the emerging impact of chemoinformatics in chemistry	7
Evaluating ligand docking methods for drugging protein–protein interfaces: insights from AlphaFold2 and molecular dynamics refinement	6
Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture	6
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	6
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	6
Development of a chemogenomics library for phenotypic screening	6
DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data	6
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	6
Evaluating the generalizability of graph neural networks for predicting collision cross section	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
Positional embeddings and zero-shot learning using BERT for molecular-property prediction	6
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	6
Multi-modal contrastive drug synergy prediction model guided by single modality	6
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions	6
hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses	6
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	6
Context-dependent similarity analysis of analogue series for structure–activity relationship transfer based on a concept from natural language processing	6
A look back at a pilot of the citation typing ontology	6
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	6
MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model	5
Art driven by visual representations of chemical space	5
Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator	5
InertDB as a generative AI-expanded resource of biologically inactive small molecules from PubChem	5
Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability	5
Development of machine learning classifiers to predict compound activity on prostate cancer cell lines	5
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data	5
Generalizable, fast, and accurate DeepQSPR with fastprop	5
Predicting protein network topology clusters from chemical structure using deep learning	5
A new workflow for the effective curation of membrane permeability data from open ADME information	5
Accelerating the inference of string generation-based chemical reaction models for industrial applications	5
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	5
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)	5
Molecular generation by Fast Assembly of (Deep)SMILES fragments	5
Identifying uncertainty in physical–chemical property estimation with IFSQSAR	5