Journal of Cheminformatics

Article	Citations
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint	148
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	97
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	81
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	80
Generating diversity and securing completeness in algorithmic retrosynthesis	78
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	70
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	66
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	63
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	62
Transformer-based molecular optimization beyond matched molecular pairs	59
Explainable uncertainty quantifications for deep learning-based molecular property prediction	54
Assessing interaction recovery of predicted protein-ligand poses	53
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	53
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	51
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	50
Paths to cheminformatics: Q&A with Ann M. Richard	49
MolPrice: assessing synthetic accessibility of molecules based on market value	47
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	47
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	45
NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products	44
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	44
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling	43
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	39
Novel molecule design with POWGAN, a policy-optimized Wasserstein generative adversarial network	39
Machine learning to predict food effects during drug development: a comprehensive review	38

AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	38
VSFlow: an open-source ligand-based virtual screening tool	38
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	37
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	36
One chiral fingerprint to find them all	36
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	36
Shinyscreen: mass spectrometry data inspection and quality checking utility	35
Deep learning of multimodal networks with topological regularization for drug repositioning	35
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	35
Crossover operators for molecular graphs with an application to virtual drug screening	35
Implementation of an open chemistry knowledge base with a Semantic Wiki	34
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	33
A quantum chemical dataset of interacting molecular pairs for chemical reaction studies	33
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	33
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	33
Bitter peptide prediction using graph neural networks	32
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	31
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	30
Prediction model for chemical explosion consequences via multimodal feature fusion	30
PyL3dMD: Python LAMMPS 3D molecular descriptors package	29
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	28
PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation	28
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	27
ProjFusNet: deep neural network for peptide precursor prediction using projection-fused protein language model and structural features	27
Accurate structure-activity relationship prediction of antioxidant peptides using a multimodal deep learning framework	27
The development of the generative adversarial supporting vector machine for molecular property generation	27
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	27
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	27
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	26
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	26
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	25
Ionization efficiency prediction of electrospray ionization mass spectrometry analytes based on molecular fingerprints and cumulative neutral losses	25
Diversifying cheminformatics	25
A systematic review of deep learning chemical language models in recent era	25
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	25
Summarizing relationships between chemicals, genes, proteins, and diseases in PubChem using analysis of their co-occurrences in patents	25
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	25
canSAR chemistry registration and standardization pipeline	25
VGSC-DB: an online database of voltage-gated sodium channels	24
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	24
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	24
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	23
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver	23
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices	23
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata	23
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	22
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	22
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	22
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	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
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)	21
Visualising lead optimisation series using reduced graphs	21
Chemical reaction network knowledge graphs: the OntoRXN ontology	20
Application of deep metric learning to molecular graph similarity	20
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	20
Reaction rebalancing: a novel approach to curating reaction databases	20
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	20
The specification game: rethinking the evaluation of drug response prediction for precision oncology	20
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	20
Subgrapher: visual fingerprinting of chemical structures	20
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach	19
Activity cliff-aware reinforcement learning for de novo drug design	19
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	19
Automatic molecular fragmentation by evolutionary optimisation	19
Deepmol: an automated machine and deep learning framework for computational chemistry	18
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	18
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	18
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	18
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	18
A transformer based generative chemical language AI model for structural elucidation of organic compounds	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	17
Searching chemical databases in the pre-history of cheminformatics	17
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	17
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	17
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	17
piscesCSM: prediction of anticancer synergistic drug combinations	17
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	16
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	16
MolNexTR: a generalized deep learning model for molecular image recognition	16
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	16
Correction: Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries	16
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	16
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	16
Enhancing molecular property prediction with quantized GNN models	16
Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability	16
Integrating synthetic accessibility with AI-based generative drug design	15
VitroBert: modeling DILI by pretraining BERT on in vitro data	15
TB-IECS: an accurate machine learning-based scoring function for virtual screening	15
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	15
UnCorrupt SMILES: a novel approach to de novo design	15
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	14
Human-in-the-loop active learning for goal-oriented molecule generation	14
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	14
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	14
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	14
Decrypting orphan GPCR drug discovery via multitask learning	14
DECIMER—hand-drawn molecule images dataset	14
What makes a reaction network “chemical”?	14
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	14
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement	14
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	14
Advancing material property prediction: using physics-informed machine learning models for viscosity	14
Automated molecular structure segmentation from documents using ChemSAM	14
Predicting the critical micelle concentration of binary surfactant mixtures using machine learning	13
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	13
Nipah Virus Inhibitor Knowledgebase (NVIK): a combined evidence approach to prioritise small molecule inhibitors	13
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	13
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	13
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	13
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data	13
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
VNFlow: integration of variational autoencoders and normalizing flows for novel molecular design	13
SMILES all around: structure to SMILES conversion for transition metal complexes	13
PIKAChU: a Python-based informatics kit for analysing chemical units	13
OWSum: algorithmic odor prediction and insight into structure-odor relationships	13
ReMODE: a deep learning-based web server for target-specific drug design	13
Prediction of UGT-mediated phase II metabolism via ligand- and structure-based predictive models	13
Application of machine reading comprehension techniques for named entity recognition in materials science	13
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	13
Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries	12
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	12
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	12
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors	12
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	12
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	12
Uncovering molecular determinants of potency and binding affinity in hit compounds targeting FGF14/Nav1.6 complex	12
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning	12

From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	12
PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules	12
Evaluation of chirality descriptors derived from SMILES heteroencoders	12
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models	12
Capsule graph networks for accurate and interpretable crystalline materials property prediction	12
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling	12
HobPre: accurate prediction of human oral bioavailability for small molecules	11
kMoL: an open-source machine and federated learning library for drug discovery	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
Integrating QSAR modelling with reinforcement learning for Syk inhibitor discovery	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
Building shape-focused pharmacophore models for effective docking screening	11
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties	11
Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors	11
Large language models open new way of AI-assisted molecule design for chemists	10
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	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
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	10
Double-head transformer neural network for molecular property prediction	10
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design	10
Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching	10
Machine learning-driven generation and screening of potential ionic liquids for cellulose dissolution	10
TraceMetrix: a traceable metabolomics interactive analysis platform	10
Advantages of two quantum programming platforms in quantum computing and quantum chemistry	10
A molecule perturbation software library and its application to study the effects of molecular design constraints	10
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	9
Improving the performance of models for one-step retrosynthesis through re-ranking	9
Combatting over-specialization bias in growing chemical databases	9
Classification of battery compounds using structure-free Mendeleev encodings	9
PubChem synonym filtering process using crowdsourcing	9
Contrastive explanations for machine learning predictions in chemistry	9
Relative molecule self-attention transformer	9
InflamNat: web-based database and predictor of anti-inflammatory natural products	9
StreaMD: the toolkit for high-throughput molecular dynamics simulations	9
Explaining and avoiding failure modes in goal-directed generation of small molecules	9
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	9
Matched pairs demonstrate robustness against inter-assay variability	9
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	9
COMA: efficient structure-constrained molecular generation using contractive and margin losses	9
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates	9
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data	9
A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles	9
Barlow Twins deep neural network for advanced 1D drug–target interaction prediction	9
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	9
Reproducible MS/MS library cleaning pipeline in matchms	8
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	8
Exploring QSAR models for activity-cliff prediction	8
xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides	8
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation	8
Unveiling polyphenol-protein interactions: a comprehensive computational analysis	8
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	8
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	8
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	8
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB	8
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	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
Improved estimation of intrinsic solubility of drug-like molecules through multi-task graph transformer	8
DeepRNA-DTI: a deep learning approach for RNA-compound interaction prediction with binding site interpretability	8
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry	8
Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture	7
Positional embeddings and zero-shot learning using BERT for molecular-property prediction	7
Evaluating the generalizability of graph neural networks for predicting collision cross section	7
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	7
Evaluating ligand docking methods for drugging protein–protein interfaces: insights from AlphaFold2 and molecular dynamics refinement	7
hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses	7
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization	7
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model	7
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	7
From molecules to data: the emerging impact of chemoinformatics in chemistry	7
Investigation of the structure-odor relationship using a Transformer model	7
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis	7
Multi-fidelity graph neural networks for predicting toluene/water partition coefficients	7
Enhancing multi-task in vivo toxicity prediction via integrated knowledge transfer of chemical knowledge and in vitro toxicity information	7
SMPR: a structure-enhanced multimodal drug‒disease prediction model for drug repositioning and cold start	7
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions	7
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling	7
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	7
Box embeddings for extending ontologies: a data-driven and interpretable approach	7
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package	7
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	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
Application of the digital annealer unit in optimizing chemical reaction conditions for enhanced production yields	7
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data	6
Predicting protein network topology clusters from chemical structure using deep learning	6
A look back at a pilot of the citation typing ontology	6
A new workflow for the effective curation of membrane permeability data from open ADME information	6
Accelerating the inference of string generation-based chemical reaction models for industrial applications	6
Biomedical data analyses facilitated by open cheminformatics workflows	6
Multi-modal contrastive drug synergy prediction model guided by single modality	6
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	6
Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator	6
Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability	6