Journal of Cheminformatics

Article	Citations
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	262
Generating diversity and securing completeness in algorithmic retrosynthesis	147
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	136
Evolve with your research: stepwise system evolution from document-driven to fact-centric research data management in materials science	123
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint	99
ANNalog: generation of MedChem-similar molecules	90
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	80
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	77
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	76
Assessing interaction recovery of predicted protein-ligand poses	71
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	69
ExPO: an exposure-conditioned neural operator for L1000 signature prediction	67
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	66
Explainable uncertainty quantifications for deep learning-based molecular property prediction	64
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	63
Novel molecular design via a scaffold-aware transformer with multi-scale attention mechanisms	60
MolPrice: assessing synthetic accessibility of molecules based on market value	60
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling	58
Paths to cheminformatics: Q&A with Ann M. Richard	57
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	57
Novel molecule design with POWGAN, a policy-optimized Wasserstein generative adversarial network	57
NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products	55
Privileged structure-based molecular fingerprints for organic electronic materials: towards intuitive machine learning interpretation	54
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	53
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	51

AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	49
One chiral fingerprint to find them all	49
Machine learning to predict food effects during drug development: a comprehensive review	49
Deep learning of multimodal networks with topological regularization for drug repositioning	48
VSFlow: an open-source ligand-based virtual screening tool	46
EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties	46
AdaptMol: domain adaptation for molecular image recognition with limited supervision	44
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	44
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	42
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	41
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	41
Collision-free morgan fingerprints: a principled approach to enhance machine learning performance and interpretability in chemistry	40
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	40
A quantum chemical dataset of interacting molecular pairs for chemical reaction studies	39
Crossover operators for molecular graphs with an application to virtual drug screening	39
Implementation of an open chemistry knowledge base with a Semantic Wiki	38
Shinyscreen: mass spectrometry data inspection and quality checking utility	36
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	36
Bitter peptide prediction using graph neural networks	35
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	35
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	34
Transformers for molecular property prediction: domain adaptation efficiently improves performance	34
ProjFusNet: deep neural network for peptide precursor prediction using projection-fused protein language model and structural features	33
PyL3dMD: Python LAMMPS 3D molecular descriptors package	33
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	33
Summarizing relationships between chemicals, genes, proteins, and diseases in PubChem using analysis of their co-occurrences in patents	32
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	32
Ionization efficiency prediction of electrospray ionization mass spectrometry analytes based on molecular fingerprints and cumulative neutral losses	32
A comprehensive evaluation of advanced methods for identifying structural alerts using extensive toxicity data	32
PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation	31
ProQSAR: A modular and reproducible framework for small-data QSAR modeling with fit-and-use models	31
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	31
How quantum-chemical geometry optimization level affects classical 3D descriptors and QSAR performance: a comparative study	31
Prediction model for chemical explosion consequences via multimodal feature fusion	31
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	31
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	31
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	30
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	30
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	29
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	29
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	29
The development of the generative adversarial supporting vector machine for molecular property generation	29
Transformer-based molecular fragment prediction using SMILES and DeepSMILES representations in a fragment-based drug discovery pipeline	29
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	28
A systematic review of deep learning chemical language models in recent era	28
Accurate structure-activity relationship prediction of antioxidant peptides using a multimodal deep learning framework	28
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices	27
VGSC-DB: an online database of voltage-gated sodium channels	27
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	27
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata	27

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	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	26
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver	25
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)	25
Implementation of a soft grading system for chemistry in a Moodle plugin	24
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	24
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	24
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	23
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	23
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	23
Subgrapher: visual fingerprinting of chemical structures	23
Reaction rebalancing: a novel approach to curating reaction databases	23
The specification game: rethinking the evaluation of drug response prediction for precision oncology	23
Automatic molecular fragmentation by evolutionary optimisation	23
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	22
Activity cliff-aware reinforcement learning for de novo drug design	22
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	22
Visualising lead optimisation series using reduced graphs	22
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	22
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach	22
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	21
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	21
A transformer based generative chemical language AI model for structural elucidation of organic compounds	21
SPARFlow: a KNIME workflow for integrated structure–activity or structure–property relationship analysis	21
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	21
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	21
Correction: Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries	20
How well can off-the-shelf LLMs elucidate molecular structures from mass spectra using chain-of-thought reasoning?	20
Multimodal graph fusion with statistically guided parsimonious descriptor selection for molecular property prediction	20
Deepmol: an automated machine and deep learning framework for computational chemistry	20
UnCorrupt SMILES: a novel approach to de novo design	20
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	20
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	20
Searching chemical databases in the pre-history of cheminformatics	19
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	19
MolNexTR: a generalized deep learning model for molecular image recognition	19
Torsion angular bin strings: algorithmic update and additional validation	19
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	19
piscesCSM: prediction of anticancer synergistic drug combinations	19
Multiscale analysis and optimal glioma therapeutic candidate discovery using the CANDO platform	19
Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability	19
TB-IECS: an accurate machine learning-based scoring function for virtual screening	18
MolMeDB RDF: transforming a relational database about biological membranes to the RDF format to increase interoperability	18
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	18
Integrating synthetic accessibility with AI-based generative drug design	18
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	18
VitroBert: modeling DILI by pretraining BERT on in vitro data	18
Enhancing molecular property prediction with quantized GNN models	18
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	18
Contrastive representation learning and capsule networks enable accurate identification of ferroptosis-related proteins	18
RGReco: a unified framework for automated R-group recognition in chemical publications	18
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	17
Predicting fire consequences with the transformer model based on multimodal feature fusion	17
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement	17
Assessing the factors influencing the quality of pocket-conditioned 3D generative models	17
Advancing material property prediction: using physics-informed machine learning models for viscosity	17
strainedSMILES2xyz: a workflow for reliable 3D structures of strained molecules from SMILES	17
Decrypting orphan GPCR drug discovery via multitask learning	17
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	16
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	16
Nipah Virus Inhibitor Knowledgebase (NVIK): a combined evidence approach to prioritise small molecule inhibitors	16
Correction: Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	16
Human-in-the-loop active learning for goal-oriented molecule generation	16
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	16
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	16
What makes a reaction network “chemical”?	16
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	16
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	16
OWSum: algorithmic odor prediction and insight into structure-odor relationships	16
OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics	15
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	15
SMILES all around: structure to SMILES conversion for transition metal complexes	15
Prediction of UGT-mediated phase II metabolism via ligand- and structure-based predictive models	15
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	15
VNFlow: integration of variational autoencoders and normalizing flows for novel molecular design	15
ReMODE: a deep learning-based web server for target-specific drug design	15
Automated molecular structure segmentation from documents using ChemSAM	15
Solvent flashcards: a visualisation tool for sustainable chemistry	15
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	15

Application of machine reading comprehension techniques for named entity recognition in materials science	15
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	14
Uncovering molecular determinants of potency and binding affinity in hit compounds targeting FGF14/Nav1.6 complex	14
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	14
Evaluation of deep learning architectures for predicting ligand interactions with neurologically relevant GPCRs	14
Predicting the critical micelle concentration of binary surfactant mixtures using machine learning	14
Evaluation of chirality descriptors derived from SMILES heteroencoders	14
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	14
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	14
Improving protein-ligand complex generation with force field guidance	14