OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Cheminformatics is 33. 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

HobPre: accurate prediction of human oral bioavailability for small molecules	35
InChI version 1.06: now more than 99.99% reliable	35
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	35
A fingerprints based molecular property prediction method using the BERT model	34
Learning protein-ligand binding affinity with atomic environment vectors	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