Journal of Cheminformatics

Article	Citations
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	230
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	108
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	85
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	80
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	77
Transformer-based molecular optimization beyond matched molecular pairs	72
Explainable uncertainty quantifications for deep learning-based molecular property prediction	66
Generating diversity and securing completeness in algorithmic retrosynthesis	65
Assessing interaction recovery of predicted protein-ligand poses	63
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	61
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	57
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	56
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	54
Paths to cheminformatics: Q&A with Ann M. Richard	53
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	51
VSFlow: an open-source ligand-based virtual screening tool	49
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	49
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	49
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	48
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	45
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	45
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	44
One chiral fingerprint to find them all	44
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	43
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	41

MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	40
Deep learning of multimodal networks with topological regularization for drug repositioning	39
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	39
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	38
Implementation of an open chemistry knowledge base with a Semantic Wiki	38
Crossover operators for molecular graphs with an application to virtual drug screening	37
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	37
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	36
Shinyscreen: mass spectrometry data inspection and quality checking utility	34
Splitting chemical structure data sets for federated privacy-preserving machine learning	32
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	32
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	32
Bitter peptide prediction using graph neural networks	32
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	30
PyL3dMD: Python LAMMPS 3D molecular descriptors package	30
canSAR chemistry registration and standardization pipeline	30
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	30
The development of the generative adversarial supporting vector machine for molecular property generation	29
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	28
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	28
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	27
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	27
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	26
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	26
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	26
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	25
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	25
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	25
Diversifying cheminformatics	25
A systematic review of deep learning chemical language models in recent era	25
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	25
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	24
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	24
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	24
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	24
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)	23
VGSC-DB: an online database of voltage-gated sodium channels	23
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	22
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	22
Implementation of a soft grading system for chemistry in a Moodle plugin	22
Activity cliff-aware reinforcement learning for de novo drug design	21
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	21
Chemical reaction network knowledge graphs: the OntoRXN ontology	21
Automatic molecular fragmentation by evolutionary optimisation	21
Reaction rebalancing: a novel approach to curating reaction databases	21
Visualising lead optimisation series using reduced graphs	21
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	21
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty	20
The specification game: rethinking the evaluation of drug response prediction for precision oncology	20

DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	20
Application of deep metric learning to molecular graph similarity	20
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	20
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	20
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	20
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	19
A transformer based generative chemical language AI model for structural elucidation of organic compounds	19
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	19
Learning protein-ligand binding affinity with atomic environment vectors	19
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	19
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	18
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	18
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	17
Searching chemical databases in the pre-history of cheminformatics	17
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	17
piscesCSM: prediction of anticancer synergistic drug combinations	17
Deepmol: an automated machine and deep learning framework for computational chemistry	17
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	17
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	16
Integrating synthetic accessibility with AI-based generative drug design	15
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	15
UnCorrupt SMILES: a novel approach to de novo design	15
MolNexTR: a generalized deep learning model for molecular image recognition	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
Enhancing molecular property prediction with quantized GNN models	15
TB-IECS: an accurate machine learning-based scoring function for virtual screening	15
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	14
QPHAR: quantitative pharmacophore activity relationship: method and validation	14
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	14
What makes a reaction network “chemical”?	14
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	14
DECIMER—hand-drawn molecule images dataset	14
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	14
Human-in-the-loop active learning for goal-oriented molecule generation	14
Decrypting orphan GPCR drug discovery via multitask learning	14
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	14
The effect of noise on the predictive limit of QSAR models	14
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	13
Solvent flashcards: a visualisation tool for sustainable chemistry	13
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	13
ReMODE: a deep learning-based web server for target-specific drug design	13
Automated molecular structure segmentation from documents using ChemSAM	13
SMILES all around: structure to SMILES conversion for transition metal complexes	13
Advancing material property prediction: using physics-informed machine learning models for viscosity	13
Application of machine reading comprehension techniques for named entity recognition in materials science	12
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	12
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	12
How can SHAP values help to shape metabolic stability of chemical compounds?	12
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	12
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	12
OWSum: algorithmic odor prediction and insight into structure-odor relationships	12
PIKAChU: a Python-based informatics kit for analysing chemical units	12
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors	11
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling	11
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	11
Correction: Reconstruction of lossless molecular representations from fingerprints	11
E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays	11
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data	11
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	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
Large language models open new way of AI-assisted molecule design for chemists	11
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling	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
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data	11
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	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
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties	10
Building shape-focused pharmacophore models for effective docking screening	10
Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching	10
kMoL: an open-source machine and federated learning library for drug discovery	10
HobPre: accurate prediction of human oral bioavailability for small molecules	10
COMA: efficient structure-constrained molecular generation using contractive and margin losses	10

Machine learning-driven generation and screening of potential ionic liquids for cellulose dissolution	10
Deep scaffold hopping with multimodal transformer neural networks	10
Prediction of blood–brain barrier and Caco-2 permeability through the Enalos Cloud Platform: combining contrastive learning and atom-attention message passing neural networks	10
Benchmarking molecular conformer augmentation with context-enriched training: graph-based transformer versus GNN models	10
PUResNet: prediction of protein-ligand binding sites using deep residual neural network	10
Advantages of two quantum programming platforms in quantum computing and quantum chemistry	9
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	9
Processing binding data using an open-source workflow	9
Double-head transformer neural network for molecular property prediction	9
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability	9
PubChem synonym filtering process using crowdsourcing	9
A molecule perturbation software library and its application to study the effects of molecular design constraints	9
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	9
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	9
Combatting over-specialization bias in growing chemical databases	9
Improving VAE based molecular representations for compound property prediction	9
Relative molecule self-attention transformer	9
InflamNat: web-based database and predictor of anti-inflammatory natural products	9
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	9
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design	9
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	9
Classification of battery compounds using structure-free Mendeleev encodings	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
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	8
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
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations	8
Reproducible MS/MS library cleaning pipeline in matchms	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
Matched pairs demonstrate robustness against inter-assay variability	8
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	8
Improving the performance of models for one-step retrosynthesis through re-ranking	8
StreaMD: the toolkit for high-throughput molecular dynamics simulations	8
Exploring QSAR models for activity-cliff prediction	7
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	7
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions	7
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	7
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model	7
Positional embeddings and zero-shot learning using BERT for molecular-property prediction	7
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry	7
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	7
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	7
QSPR modeling of selectivity at infinite dilution of ionic liquids	7
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	7
Evaluating the generalizability of graph neural networks for predicting collision cross section	7
Investigation of the structure-odor relationship using a Transformer model	7
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	7
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis	7
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB	7
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	7
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package	7
Unveiling polyphenol-protein interactions: a comprehensive computational analysis	7
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	7
“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	7
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	7
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation	7
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization	6
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	6
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling	6
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data	6
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop	6
Application of the digital annealer unit in optimizing chemical reaction conditions for enhanced production yields	6
hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses	6
Accelerating the inference of string generation-based chemical reaction models for industrial applications	6
Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability	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
A look back at a pilot of the citation typing ontology	6
Identifying uncertainty in physical–chemical property estimation with IFSQSAR	6
Development of machine learning classifiers to predict compound activity on prostate cancer cell lines	6
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	5
Biomedical data analyses facilitated by open cheminformatics workflows	5
Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model	5
ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction	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
Molecular generation by Fast Assembly of (Deep)SMILES fragments	5
Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence	5
Efficient virtual high-content screening using a distance-aware transformer model	5
Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator	5
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	5
DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data	5
Context-dependent similarity analysis of analogue series for structure–activity relationship transfer based on a concept from natural language processing	5
Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction	5
InertDB as a generative AI-expanded resource of biologically inactive small molecules from PubChem	5
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)	5
Development of a chemogenomics library for phenotypic screening	5
MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model	5
ELNdataBridge: facilitating data exchange and collaboration by linking Electronic Lab Notebooks via API	4
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification	4
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis	4
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states	4
DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning	4
Two years of explicit CiTO annotations	4