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 2021-09-01 to 2025-09-01.)

Article	Citations
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	239
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	110
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	88
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	88
Generating diversity and securing completeness in algorithmic retrosynthesis	82
Assessing interaction recovery of predicted protein-ligand poses	74
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	68
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	67
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	65
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	65
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	58
Explainable uncertainty quantifications for deep learning-based molecular property prediction	58
Transformer-based molecular optimization beyond matched molecular pairs	57
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint	57
Paths to cheminformatics: Q&A with Ann M. Richard	51
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	51
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	48
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	46
Deep learning of multimodal networks with topological regularization for drug repositioning	46
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling	46
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	45
VSFlow: an open-source ligand-based virtual screening tool	44
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	41
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	41
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	41

One chiral fingerprint to find them all	40
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	39
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	38
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	38
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	36
Implementation of an open chemistry knowledge base with a Semantic Wiki	36
Crossover operators for molecular graphs with an application to virtual drug screening	34
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	34
Splitting chemical structure data sets for federated privacy-preserving machine learning	32
Shinyscreen: mass spectrometry data inspection and quality checking utility	32
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	32
Bitter peptide prediction using graph neural networks	31
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	30
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	30
PyL3dMD: Python LAMMPS 3D molecular descriptors package	29
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	29
The development of the generative adversarial supporting vector machine for molecular property generation	28
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	28
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	28
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	28
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	28
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	27
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	26
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	26
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	26
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	26
canSAR chemistry registration and standardization pipeline	26
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	26
Prediction model for chemical explosion consequences via multimodal feature fusion	25
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	25
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	25
Diversifying cheminformatics	24
A systematic review of deep learning chemical language models in recent era	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	23
VGSC-DB: an online database of voltage-gated sodium channels	23
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	23
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	23
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	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)	23
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver	22
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	22
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	21
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	21
Reaction rebalancing: a novel approach to curating reaction databases	21
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	20
The specification game: rethinking the evaluation of drug response prediction for precision oncology	20
Visualising lead optimisation series using reduced graphs	20

YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	20
Activity cliff-aware reinforcement learning for de novo drug design	20
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
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	20
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach	20
Automatic molecular fragmentation by evolutionary optimisation	20
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	19
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	18
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	18
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	18
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	18
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	18
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	17
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	17
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	16
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	16
Deepmol: an automated machine and deep learning framework for computational chemistry	16
MolNexTR: a generalized deep learning model for molecular image recognition	15
Enhancing molecular property prediction with quantized GNN models	15
UnCorrupt SMILES: a novel approach to de novo design	15
Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability	15
Searching chemical databases in the pre-history of cheminformatics	15
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?	15
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	15
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	15
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	15
A transformer based generative chemical language AI model for structural elucidation of organic compounds	15
piscesCSM: prediction of anticancer synergistic drug combinations	15
Decrypting orphan GPCR drug discovery via multitask learning	14
What makes a reaction network “chemical”?	14
Integrating synthetic accessibility with AI-based generative drug design	14
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement	14
VitroBert: modeling DILI by pretraining BERT on in vitro data	14
TB-IECS: an accurate machine learning-based scoring function for virtual screening	14
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	14
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	14
Human-in-the-loop active learning for goal-oriented molecule generation	14
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	14
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	13
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	13
Solvent flashcards: a visualisation tool for sustainable chemistry	13
The effect of noise on the predictive limit of QSAR models	13
Advancing material property prediction: using physics-informed machine learning models for viscosity	13
DECIMER—hand-drawn molecule images dataset	13
ReMODE: a deep learning-based web server for target-specific drug design	13
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	12
Application of machine reading comprehension techniques for named entity recognition in materials science	12
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	12
Automated molecular structure segmentation from documents using ChemSAM	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
OWSum: algorithmic odor prediction and insight into structure-odor relationships	12
PIKAChU: a Python-based informatics kit for analysing chemical units	12
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	12
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	12
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	12
SMILES all around: structure to SMILES conversion for transition metal complexes	12
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
How can SHAP values help to shape metabolic stability of chemical compounds?	12
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	12