Journal of Cheminformatics

Article	Citations
Improving route development using convergent retrosynthesis planning	343
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	188
Robustness under parameter and problem domain alterations of Bayesian optimization methods for chemical reactions	90
Double-head transformer neural network for molecular property prediction	76
Explainable uncertainty quantifications for deep learning-based molecular property prediction	69
Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models	68
Improving drug repositioning with negative data labeling using large language models	57
Deepmol: an automated machine and deep learning framework for computational chemistry	50
RanDepict: Random chemical structure depiction generator	49
Structure-based, deep-learning models for protein-ligand binding affinity prediction	48
Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B	47
One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data	47
Processing binding data using an open-source workflow	46
ProfhEX: AI-based platform for small molecules liability profiling	46
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	43
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	43
Consensus holistic virtual screening for drug discovery: a novel machine learning model approach	43
Prediction of Pt, Ir, Ru, and Rh complexes light absorption in the therapeutic window for phototherapy using machine learning	41
Anticipating protein evolution with successor sequence predictor	41
RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking	41
Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy	40
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	40
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	39
ChemTables: a dataset for semantic classification on tables in chemical patents	38
Reply to “FAIR chemical structure in the Journal of Cheminformatics”	38

European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	38
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	37
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	36
Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics’ Scientific Contribution Statement	36
COMA: efficient structure-constrained molecular generation using contractive and margin losses	36
Individual and collective human intelligence in drug design: evaluating the search strategy	34
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	34
CPSign: conformal prediction for cheminformatics modeling	33
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	32
A molecule perturbation software library and its application to study the effects of molecular design constraints	32
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability	32
RAIChU: automating the visualisation of natural product biosynthesis	31
DrugTax: package for drug taxonomy identification and explainable feature extraction	31
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	30
EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency	30
Learning protein-ligand binding affinity with atomic environment vectors	29
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons	29
MORTAR: a rich client application for in silico molecule fragmentation	27
Machine intelligence-driven framework for optimized hit selection in virtual screening	25
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study	25
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES	25
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	25
Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening	24
Implementation of a soft grading system for chemistry in a Moodle plugin: reaction handling	24
Transformer-based molecular optimization beyond matched molecular pairs	23
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules	23
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	23
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	21
Cobdock: an accurate and practical machine learning-based consensus blind docking method	21
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures	21
cidalsDB: an AI-empowered platform for anti-pathogen therapeutics research	21
STOUT: SMILES to IUPAC names using neural machine translation	21
Improving chemical reaction yield prediction using pre-trained graph neural networks	21
Correction to: Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs	21
Sort & Slice: a simple and superior alternative to hash-based folding for extended-connectivity fingerprints	21
FAIR chemical structures in the Journal of Cheminformatics	20
Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence	20
Surge: a fast open-source chemical graph generator	20
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	19
IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra	19
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	19
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	19
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	18
Three pillars for ensuring public access and integrity of chemical databases powering cheminformatics	18
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	18
GNINA 1.0: molecular docking with deep learning	18
Relative molecule self-attention transformer	18
InflamNat: web-based database and predictor of anti-inflammatory natural products	18
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design	18
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer	17

Correction: APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	17
A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence	17
Reproducible MS/MS library cleaning pipeline in matchms	17
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	17
BBB-PEP-prediction: improved computational model for identification of blood–brain barrier peptides using blending position relative composition specific features and ensemble modeling	16
Paths to cheminformatics: Q&A with Ann M. Richard	16
Combatting over-specialization bias in growing chemical databases	16
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	16
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates	16
Searching chemical databases in the pre-history of cheminformatics	16
Paths to cheminformatics: Q&A with Nathaniel Charest	16
Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment	16
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	15
DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning	15
Evaluation of reinforcement learning in transformer-based molecular design	15
Improving VAE based molecular representations for compound property prediction	15
Matched pairs demonstrate robustness against inter-assay variability	15
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations	14
Machine learning for identification of silylated derivatives from mass spectra	14
piscesCSM: prediction of anticancer synergistic drug combinations	14
“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool	14
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	14
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	14
LigninGraphs: lignin structure determination with multiscale graph modeling	14
VSFlow: an open-source ligand-based virtual screening tool	13
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis	13
A numerical compass for experiment design in chemical kinetics and molecular property estimation	13
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data	13
Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow	13
Explaining and avoiding failure modes in goal-directed generation of small molecules	13
A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles	13
Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles	13
StreaMD: the toolkit for high-throughput molecular dynamics simulations	12
Improving the performance of models for one-step retrosynthesis through re-ranking	12
Exploring QSAR models for activity-cliff prediction	12
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification	12
TB-IECS: an accurate machine learning-based scoring function for virtual screening	12
Correction: Global reactivity models are impactful in industrial synthesis applications	12
PubChem synonym filtering process using crowdsourcing	12
One chiral fingerprint to find them all	12
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	12
Ensemble completeness in conformer sampling: the case of small macrocycles	11
Simultaneously improving accuracy and computational cost under parametric constraints in materials property prediction tasks	11
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	11
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	11
MolNexTR: a generalized deep learning model for molecular image recognition	11
PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction	11
MDSuite: comprehensive post-processing tool for particle simulations	11
Deep learning of multimodal networks with topological regularization for drug repositioning	11
Confidence bands and hypothesis tests for hit enrichment curves	11
CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space	11
HD_BPMDS: a curated binary pattern multitarget dataset of Huntington’s disease–targeting agents	11
Barlow Twins deep neural network for advanced 1D drug–target interaction prediction	10
Classification of battery compounds using structure-free Mendeleev encodings	10
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	10
Effectiveness of molecular fingerprints for exploring the chemical space of natural products	10
ROASMI: accelerating small molecule identification by repurposing retention data	10
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms	10
Integrating synthetic accessibility with AI-based generative drug design	10
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	10
SANCDB: an update on South African natural compounds and their readily available analogs	10
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	10
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	10
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	10
HybridGCN for protein solubility prediction with adaptive weighting of multiple features	10
ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction	9
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	9
Two years of explicit CiTO annotations	9
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	9
UnCorrupt SMILES: a novel approach to de novo design	9
MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry	9
Visualizing chemical space networks with RDKit and NetworkX	9
LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP	9
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	9
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	9
Sequence-based prediction of protein binding regions and drug–target interactions	9
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states	8
QSPR modeling of selectivity at infinite dilution of ionic liquids	8
Correction to: Optimized SQE atomic charges for peptides accessible via a web application	8
Twitter integration of chemistry software tools	8

AiGPro: a multi-tasks model for profiling of GPCRs for agonist and antagonist	8
Paths to Cheminformatics: Q&A with Norberto Sánchez-Cruz and Emma Schymanski	8
QPHAR: quantitative pharmacophore activity relationship: method and validation	8
The effect of noise on the predictive limit of QSAR models	8
Optimized SQE atomic charges for peptides accessible via a web application	8
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	8
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning	8
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis	7
FPocketWeb: protein pocket hunting in a web browser	7
An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts	7
Nonadditivity in public and inhouse data: implications for drug design	7
Bitter peptide prediction using graph neural networks	7
LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification	7
InChI isotopologue and isotopomer specifications	7
Deep generative model for drug design from protein target sequence	7
2D SIFt: a matrix of ligand-receptor interactions	7
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation	7
Patch seriation to visualize data and model parameters	7
Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data	7
Hamiltonian diversity: effectively measuring molecular diversity by shortest Hamiltonian circuits	6
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products	6
What makes a reaction network “chemical”?	6
Metis: a python-based user interface to collect expert feedback for generative chemistry models	6
Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum	6
MolPROP: Molecular Property prediction with multimodal language and graph fusion	6
Commentary: the first twelve years of the Journal of Cheminformatics	6
Adaptive language model training for molecular design	6
MetaRF: attention-based random forest for reaction yield prediction with a few trails	6
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	6
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	6
SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches	6
AdductHunter: identifying protein-metal complex adducts in mass spectra	6
DECIMER—hand-drawn molecule images dataset	6
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	6
Generative model based on junction tree variational autoencoder for HOMO value prediction and molecular optimization	6
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	6
Correction: StreaMD: the toolkit for high-throughput molecular dynamics simulations	5
Correction: QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning	5
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	5
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design	5
Stereochemically-aware bioactivity descriptors for uncharacterized chemical compounds	5
Human-in-the-loop active learning for goal-oriented molecule generation	5
LinChemIn: SynGraph—a data model and a toolkit to analyze and compare synthetic routes	5
Uncertainty-aware prediction of chemical reaction yields with graph neural networks	5
Global reactivity models are impactful in industrial synthesis applications	5
Correction: Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	5
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	5
Practical guidelines for the use of gradient boosting for molecular property prediction	5
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	5
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB	5
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	5
Quantitative structure–activity relationships of chemical bioactivity toward proteins associated with molecular initiating events of organ-specific toxicity	5
Correction: DecoyFinder, a tool for finding decoy molecules	5
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	5
CLAIRE: a contrastive learning-based predictor for EC number of chemical reactions	5
Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity	5
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	5
Chemical space as a unifying theme for chemistry	5
PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications	5
Advancing material property prediction: using physics-informed machine learning models for viscosity	4
Splitting chemical structure data sets for federated privacy-preserving machine learning	4
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry	4
A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data	4
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	4
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	4
Milestones in chemoinformatics: global view of the field	4
NMR shift prediction from small data quantities	4
Benchmarks for interpretation of QSAR models	4
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	4
Decrypting orphan GPCR drug discovery via multitask learning	4
Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology	4
Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison	4
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	4
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	4
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model	4
QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool	4
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis	4
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	4
The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction	4
Investigation of the structure-odor relationship using a Transformer model	4
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	4
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	4
“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	4