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 2020-11-01 to 2024-11-01.)

Article	Citations
COCONUT online: Collection of Open Natural Products database	305
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models	302
GNINA 1.0: molecular docking with deep learning	267
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning	164
ProLIF: a library to encode molecular interactions as fingerprints	155
patRoon: open source software platform for environmental mass spectrometry based non-target screening	118
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	70
PUResNet: prediction of protein-ligand binding sites using deep residual neural network	69
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag	67
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map	66
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	61
Memory-assisted reinforcement learning for diverse molecular de novo design	61
How can SHAP values help to shape metabolic stability of chemical compounds?	58
Molecular optimization by capturing chemist’s intuition using deep neural networks	55
Diversity oriented Deep Reinforcement Learning for targeted molecule generation	46
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	42
DECIMER 1.0: deep learning for chemical image recognition using transformers	42
Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions	41
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms	41
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology	41
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study	41
Designing optimized drug candidates with Generative Adversarial Network	39
Using GANs with adaptive training data to search for new molecules	37
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES	36
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	36

Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	35
HobPre: accurate prediction of human oral bioavailability for small molecules	35
InChI version 1.06: now more than 99.99% reliable	35
Learning protein-ligand binding affinity with atomic environment vectors	34
A fingerprints based molecular property prediction method using the BERT model	34
Benchmarks for interpretation of QSAR models	33
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics†	33
Deep scaffold hopping with multimodal transformer neural networks	33
DockStream: a docking wrapper to enhance de novo molecular design	32
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection	32
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling	31
SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors	28
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles	27
MAIP: a web service for predicting blood‐stage malaria inhibitors	27
Sequence-based prediction of protein binding regions and drug–target interactions	27
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach	26
SANCDB: an update on South African natural compounds and their readily available analogs	26
Transformer-based molecular optimization beyond matched molecular pairs	25
MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning	25
The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction	25
Explainable uncertainty quantifications for deep learning-based molecular property prediction	24
Splitting chemical structure data sets for federated privacy-preserving machine learning	23
Uncertainty-aware prediction of chemical reaction yields with graph neural networks	23
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning	23
STOUT: SMILES to IUPAC names using neural machine translation	23
Deep generative model for drug design from protein target sequence	22
Reinvent 4: Modern AI–driven generative molecule design	22
The effect of noise on the predictive limit of QSAR models	22
Using informative features in machine learning based method for COVID-19 drug repurposing	22
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling	21
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer	21
Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning	21
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	21
Too sweet: cheminformatics for deglycosylation in natural products	20
LEADD: Lamarckian evolutionary algorithm for de novo drug design	20
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data	20
Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds	20
FAIR chemical structures in the Journal of Cheminformatics	19
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification	19
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	19
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	18
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates	17
ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction	17
DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions	17
Blood–brain barrier penetration prediction enhanced by uncertainty estimation	17
Multi-PLI: interpretable multi‐task deep learning model for unifying protein–ligand interaction datasets	16
Substructure-based neural machine translation for retrosynthetic prediction	16
Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models	16
Improving the performance of models for one-step retrosynthesis through re-ranking	16

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning	16
Human-in-the-loop assisted de novo molecular design	16
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	16
Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses	16
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	16
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database	16
MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry	16
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	15
Exploring QSAR models for activity-cliff prediction	15
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning	15
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	15
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges	15
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds	14
“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool	14
Assessing the calibration in toxicological in vitro models with conformal prediction	14
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	14
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19	14
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation	14
Development and evaluation of two-parameter linear free energy models for the prediction of human skin permeability coefficient of neutral organic chemicals	13
MolData, a molecular benchmark for disease and target based machine learning	13
Practical guidelines for the use of gradient boosting for molecular property prediction	13
Systemic evolutionary chemical space exploration for drug discovery	13
Molecular generation by Fast Assembly of (Deep)SMILES fragments	13
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	13
Nonadditivity in public and inhouse data: implications for drug design	13
Probabilistic metabolite annotation using retention time prediction and meta-learned projections	13
DFFNDDS: prediction of synergistic drug combinations with dual feature fusion networks	13
DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature	13
RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions	13
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	12
IDSM ChemWebRDF: SPARQLing small-molecule datasets	12
UnCorrupt SMILES: a novel approach to de novo design	12
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics	12
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	12
MetaRF: attention-based random forest for reaction yield prediction with a few trails	12