OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Cheminformatics is 34. 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 2020-03-01 to 2024-03-01.)

Article	Citations
Review on natural products databases: where to find data in 2020	238
COCONUT online: Collection of Open Natural Products database	218
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models	208
Molecular representations in AI-driven drug discovery: a review and practical guide	189
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions	186
GNINA 1.0: molecular docking with deep learning	175
An open source chemical structure curation pipeline using RDKit	152
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome	147
Transformer-CNN: Swiss knife for QSAR modeling and interpretation	130
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning	128
SMILES-based deep generative scaffold decorator for de-novo drug design	93
patRoon: open source software platform for environmental mass spectrometry based non-target screening	90
ProLIF: a library to encode molecular interactions as fingerprints	83
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT	70
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization	66
DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques	59
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag	58
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map	54
kGCN: a graph-based deep learning framework for chemical structures	54
SYBA: Bayesian estimation of synthetic accessibility of organic compounds	52
Memory-assisted reinforcement learning for diverse molecular de novo design	51
PUResNet: prediction of protein-ligand binding sites using deep residual neural network	49
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	49
Molecular optimization by capturing chemist’s intuition using deep neural networks	44
EDock: blind protein–ligand docking by replica-exchange monte carlo simulation	44

DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach	42
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning	42
CReM: chemically reasonable mutations framework for structure generation	40
DECIMER: towards deep learning for chemical image recognition	39
Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets	39
Aromatic clusters in protein–protein and protein–drug complexes	37
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	36
Comparison and improvement of the predictability and interpretability with ensemble learning models in QSPR applications	35
Diversity oriented Deep Reinforcement Learning for targeted molecule generation	35
How can SHAP values help to shape metabolic stability of chemical compounds?	34
spyrmsd: symmetry-corrected RMSD calculations in Python	34