OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Cheminformatics is 12. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-05-01 to 2025-05-01.)

Article	Citations
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	357
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	198
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	93
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	78
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	72
Transformer-based molecular optimization beyond matched molecular pairs	69
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	58
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	51
Deep learning of multimodal networks with topological regularization for drug repositioning	50
Paths to cheminformatics: Q&A with Ann M. Richard	50
VSFlow: an open-source ligand-based virtual screening tool	50
Explainable uncertainty quantifications for deep learning-based molecular property prediction	50
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	50
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	49
One chiral fingerprint to find them all	47
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	47
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	45
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	45
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	44
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	42
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	41
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	40
Bitter peptide prediction using graph neural networks	39
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	39
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	38

Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	38
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	38
PyL3dMD: Python LAMMPS 3D molecular descriptors package	37
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	37
Splitting chemical structure data sets for federated privacy-preserving machine learning	37
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	35
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	35
canSAR chemistry registration and standardization pipeline	35
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	33
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	33
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	32
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	32
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	31
A systematic review of deep learning chemical language models in recent era	30
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	28
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	28
Diversifying cheminformatics	27
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	27
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	26
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	26
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	25
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	25
VGSC-DB: an online database of voltage-gated sodium channels	24
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	24
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds	23
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	23
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)	22
The specification game: rethinking the evaluation of drug response prediction for precision oncology	21
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	21
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	21
Implementation of a soft grading system for chemistry in a Moodle plugin	21
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	21
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	21
Reaction rebalancing: a novel approach to curating reaction databases	21
Automatic molecular fragmentation by evolutionary optimisation	21
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty	20
Application of deep metric learning to molecular graph similarity	20
A machine learning platform for the discovery of materials	20
Chemical reaction network knowledge graphs: the OntoRXN ontology	20
Visualising lead optimisation series using reduced graphs	19
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	19
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	19
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	19
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	19
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	19
Activity cliff-aware reinforcement learning for de novo drug design	19
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	19
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	19
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	19

ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	18
Ensemble completeness in conformer sampling: the case of small macrocycles	18
Learning protein-ligand binding affinity with atomic environment vectors	18
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	18
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	18
Deepmol: an automated machine and deep learning framework for computational chemistry	18
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	17
Searching chemical databases in the pre-history of cheminformatics	17
piscesCSM: prediction of anticancer synergistic drug combinations	17
TB-IECS: an accurate machine learning-based scoring function for virtual screening	17
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	17
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	16
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	16
UnCorrupt SMILES: a novel approach to de novo design	16
Integrating synthetic accessibility with AI-based generative drug design	16
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	16
MolNexTR: a generalized deep learning model for molecular image recognition	16
The effect of noise on the predictive limit of QSAR models	15
Nonadditivity in public and inhouse data: implications for drug design	15
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	15
Decrypting orphan GPCR drug discovery via multitask learning	14
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	14
DECIMER—hand-drawn molecule images dataset	14
Human-in-the-loop active learning for goal-oriented molecule generation	14
What makes a reaction network “chemical”?	14
QPHAR: quantitative pharmacophore activity relationship: method and validation	14
Advancing material property prediction: using physics-informed machine learning models for viscosity	14
ReMODE: a deep learning-based web server for target-specific drug design	13
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	13
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	13
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	13
Automated molecular structure segmentation from documents using ChemSAM	13
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	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
IDSM ChemWebRDF: SPARQLing small-molecule datasets	12
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	12
Solvent flashcards: a visualisation tool for sustainable chemistry	12
OWSum: algorithmic odor prediction and insight into structure-odor relationships	12
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	12
PIKAChU: a Python-based informatics kit for analysing chemical units	12
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models	12
How can SHAP values help to shape metabolic stability of chemical compounds?	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	12
Application of machine reading comprehension techniques for named entity recognition in materials science	12
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	12