OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Cheminformatics is 10. 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 2021-02-01 to 2025-02-01.)

Article	Citations
A molecule perturbation software library and its application to study the effects of molecular design constraints	302
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification	267
COMA: efficient structure-constrained molecular generation using contractive and margin losses	164
Robustness under parameter and problem domain alterations of Bayesian optimization methods for chemical reactions	70
STOUT: SMILES to IUPAC names using neural machine translation	69
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	67
CPSign: conformal prediction for cheminformatics modeling	66
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	61
ChemTables: a dataset for semantic classification on tables in chemical patents	58
RAIChU: automating the visualisation of natural product biosynthesis	55
Molecular optimization by capturing chemist’s intuition using deep neural networks	46
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists	46
One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data	42
Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B	42
Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics’ Scientific Contribution Statement	41
Reply to “FAIR chemical structure in the Journal of Cheminformatics”	41
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	41
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer	39
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision	37
Machine intelligence-driven framework for optimized hit selection in virtual screening	36
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta	36
Double-head transformer neural network for molecular property prediction	35
Improving chemical reaction yield prediction using pre-trained graph neural networks	35
Individual and collective human intelligence in drug design: evaluating the search strategy	35
Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening	34

Molecule Set Comparator (MSC): a CDK-based open rich‐client tool for molecule set similarity evaluations	34
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons	33
FAIR chemical structures in the Journal of Cheminformatics	33
Processing binding data using an open-source workflow	33
EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency	32
Implementation of a soft grading system for chemistry in a Moodle plugin: reaction handling	32
RanDepict: Random chemical structure depiction generator	31
Relative molecule self-attention transformer	28
Learning protein-ligand binding affinity with atomic environment vectors	27
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability	27
Transformer-based molecular optimization beyond matched molecular pairs	27
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	26
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms	26
Surge: a fast open-source chemical graph generator	25
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding	25
Structure-based, deep-learning models for protein-ligand binding affinity prediction	25
InflamNat: web-based database and predictor of anti-inflammatory natural products	24
A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence	23
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder	23
MORTAR: a rich client application for in silico molecule fragmentation	23
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL	23
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES	22
AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data	22
RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking	22
Consensus holistic virtual screening for drug discovery: a novel machine learning model approach	22
IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra	21
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	21
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	21
ChemSpectra: a web-based spectra editor for analytical data	21
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules	20
Prediction of Pt, Ir, Ru, and Rh complexes light absorption in the therapeutic window for phototherapy using machine learning	20
DrugTax: package for drug taxonomy identification and explainable feature extraction	20
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	20
Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models	19
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map	19
ProfhEX: AI-based platform for small molecules liability profiling	19
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study	18
GNINA 1.0: molecular docking with deep learning	17
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models	17
Explainable uncertainty quantifications for deep learning-based molecular property prediction	17
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures	17
Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy	16
Deepmol: an automated machine and deep learning framework for computational chemistry	16
cidalsDB: an AI-empowered platform for anti-pathogen therapeutics research	16
Cobdock: an accurate and practical machine learning-based consensus blind docking method	16
Correction to: Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs	16
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	16
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	16
Sort & Slice: a simple and superior alternative to hash-based folding for extended-connectivity fingerprints	16
Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence	16

Two years of explicit CiTO annotations	15
Ensemble completeness in conformer sampling: the case of small macrocycles	15
Visualizing chemical space networks with RDKit and NetworkX	15
Deep learning of multimodal networks with topological regularization for drug repositioning	15
HybridGCN for protein solubility prediction with adaptive weighting of multiple features	14
Simultaneously improving accuracy and computational cost under parametric constraints in materials property prediction tasks	14
Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow	14
Explaining and avoiding failure modes in goal-directed generation of small molecules	14
Paths to cheminformatics: Q&A with Ann M. Richard	14
Confidence bands and hypothesis tests for hit enrichment curves	13
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry	13
Paths to cheminformatics: Q&A with Nathaniel Charest	13
Hybrid semantic recommender system for chemical compounds in large-scale datasets	13
Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment	13
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space	13
LigninGraphs: lignin structure determination with multiscale graph modeling	13
VSFlow: an open-source ligand-based virtual screening tool	13
Evaluation of reinforcement learning in transformer-based molecular design	13
BBB-PEP-prediction: improved computational model for identification of blood–brain barrier peptides using blending position relative composition specific features and ensemble modeling	13
PubChem synonym filtering process using crowdsourcing	13
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning	13
CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space	12
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions	12
A numerical compass for experiment design in chemical kinetics and molecular property estimation	12
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis	12
SANCDB: an update on South African natural compounds and their readily available analogs	12
Matched pairs demonstrate robustness against inter-assay variability	12
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph	12
Correction: Global reactivity models are impactful in industrial synthesis applications	11
Integrating synthetic accessibility with AI-based generative drug design	11
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data	11
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms	11
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	11
ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction	11
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models	11
Combatting over-specialization bias in growing chemical databases	10
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations	10
Sequence-based prediction of protein binding regions and drug–target interactions	10
MDSuite: comprehensive post-processing tool for particle simulations	10
piscesCSM: prediction of anticancer synergistic drug combinations	10
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states	10
MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry	10
ChemProps: A RESTful API enabled database for composite polymer name standardization	10
Improving the performance of models for one-step retrosynthesis through re-ranking	10
Machine learning for identification of silylated derivatives from mass spectra	10
Reproducible MS/MS library cleaning pipeline in matchms	10
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification	10
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	10
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction	10
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer	10
Leveraging computational tools to combat malaria: assessment and development of new therapeutics	10