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 2021-11-01 to 2025-11-01.)

Article	Citations
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	120
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint	81
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors	76
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning	73
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	73
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	64
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands	63
Generating diversity and securing completeness in algorithmic retrosynthesis	62
Transformer-based molecular optimization beyond matched molecular pairs	61
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	61
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	56
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	54
Assessing interaction recovery of predicted protein-ligand poses	53
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	51
Explainable uncertainty quantifications for deep learning-based molecular property prediction	51
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions	49
Paths to cheminformatics: Q&A with Ann M. Richard	48
MolPrice: assessing synthetic accessibility of molecules based on market value	46
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	45
VSFlow: an open-source ligand-based virtual screening tool	42
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	42
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery	42
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling	42
Deep learning of multimodal networks with topological regularization for drug repositioning	40
One chiral fingerprint to find them all	38

PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	38
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action	36
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data	36
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	36
Splitting chemical structure data sets for federated privacy-preserving machine learning	35
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application	35
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples	34
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	34
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach	34
Bitter peptide prediction using graph neural networks	34
Shinyscreen: mass spectrometry data inspection and quality checking utility	33
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores	33
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	32
Crossover operators for molecular graphs with an application to virtual drug screening	32
Explaining compound activity predictions with a substructure-aware loss for graph neural networks	32
Implementation of an open chemistry knowledge base with a Semantic Wiki	32
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors	31
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion	31
Prediction model for chemical explosion consequences via multimodal feature fusion	30
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop	29
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1	29
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	28
Predictive modeling of visible-light azo-photoswitches’ properties using structural features	28
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm	28
PyL3dMD: Python LAMMPS 3D molecular descriptors package	27
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development	27
PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation	26
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts	26
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals	26
A systematic review of deep learning chemical language models in recent era	25
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
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines*	24
Diversifying cheminformatics	24
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	24
canSAR chemistry registration and standardization pipeline	24
The development of the generative adversarial supporting vector machine for molecular property generation	24
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices	23
VGSC-DB: an online database of voltage-gated sodium channels	23
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data	23
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver	23
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition	23
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank	23
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata	22
Reaction rebalancing: a novel approach to curating reaction databases	22
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)	22
Implementation of a soft grading system for chemistry in a Moodle plugin	22
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data	22
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	22
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	22
Automatic molecular fragmentation by evolutionary optimisation	21

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations	21
Ilm-NMR-P31: an open-access 31P nuclear magnetic resonance database and data-driven prediction of 31P NMR shifts	20
Chemical reaction network knowledge graphs: the OntoRXN ontology	20
Activity cliff-aware reinforcement learning for de novo drug design	20
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach	20
Visualising lead optimisation series using reduced graphs	20
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications	20
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation	19
The specification game: rethinking the evaluation of drug response prediction for precision oncology	19
Subgrapher: visual fingerprinting of chemical structures	19
Application of deep metric learning to molecular graph similarity	19
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	18
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	18
A transformer based generative chemical language AI model for structural elucidation of organic compounds	18
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	17
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	17
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	17
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models	17
Deepmol: an automated machine and deep learning framework for computational chemistry	16
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	16
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	16
Correction: Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries	15
piscesCSM: prediction of anticancer synergistic drug combinations	15
Enhancing molecular property prediction with quantized GNN models	15
TB-IECS: an accurate machine learning-based scoring function for virtual screening	15
MolNexTR: a generalized deep learning model for molecular image recognition	15
UnCorrupt SMILES: a novel approach to de novo design	15
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model	15
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	15
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	15
Integrating synthetic accessibility with AI-based generative drug 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
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	14
VitroBert: modeling DILI by pretraining BERT on in vitro data	14
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	14
DECIMER—hand-drawn molecule images dataset	14
Decrypting orphan GPCR drug discovery via multitask learning	14
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin	14
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement	14
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
LAGNet: better electron density prediction for LCAO-based data and drug-like substances	13
PIKAChU: a Python-based informatics kit for analysing chemical units	13
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation	13
Application of machine reading comprehension techniques for named entity recognition in materials science	13
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data	13
OWSum: algorithmic odor prediction and insight into structure-odor relationships	13
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening	13
Human-in-the-loop active learning for goal-oriented molecule generation	13
What makes a reaction network “chemical”?	13
Automated molecular structure segmentation from documents using ChemSAM	13
Solvent flashcards: a visualisation tool for sustainable chemistry	13
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models	12
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design	12
Prediction of UGT-mediated phase II metabolism via ligand- and structure-based predictive models	12
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature	12
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	12
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	12
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	12
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism	12
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models	12
SMILES all around: structure to SMILES conversion for transition metal complexes	12
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example	12
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials	12
Evaluation of chirality descriptors derived from SMILES heteroencoders	12
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling	12
VNFlow: integration of variational autoencoders and normalizing flows for novel molecular design	12
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management	12
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	12
ReMODE: a deep learning-based web server for target-specific drug design	12
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors	12
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data	12