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 2020-04-01 to 2024-04-01.)

Article	Citations
Review on natural products databases: where to find data in 2020	243
COCONUT online: Collection of Open Natural Products database	227
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models	215
Molecular representations in AI-driven drug discovery: a review and practical guide	202
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions	196
GNINA 1.0: molecular docking with deep learning	181
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome	157
An open source chemical structure curation pipeline using RDKit	157
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning	130
SMILES-based deep generative scaffold decorator for de-novo drug design	99
ProLIF: a library to encode molecular interactions as fingerprints	96
patRoon: open source software platform for environmental mass spectrometry based non-target screening	94
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT	72
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization	70
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
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	55
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map	55
kGCN: a graph-based deep learning framework for chemical structures	54
SYBA: Bayesian estimation of synthetic accessibility of organic compounds	53
PUResNet: prediction of protein-ligand binding sites using deep residual neural network	51
Memory-assisted reinforcement learning for diverse molecular de novo design	51
EDock: blind protein–ligand docking by replica-exchange monte carlo simulation	45
Molecular optimization by capturing chemist’s intuition using deep neural networks	44
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach	42

CReM: chemically reasonable mutations framework for structure generation	41
How can SHAP values help to shape metabolic stability of chemical compounds?	40
Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets	39
DECIMER: towards deep learning for chemical image recognition	39
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	39
Aromatic clusters in protein–protein and protein–drug complexes	38
Diversity oriented Deep Reinforcement Learning for targeted molecule generation	36
spyrmsd: symmetry-corrected RMSD calculations in Python	34
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors	34
A review of optical chemical structure recognition tools	33
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms	33
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study	32
Chemoinformatics-based enumeration of chemical libraries: a tutorial	31
DECIMER 1.0: deep learning for chemical image recognition using transformers	31
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology	30
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	30
Benchmarks for interpretation of QSAR models	30
InChI version 1.06: now more than 99.99% reliable	29
Learning protein-ligand binding affinity with atomic environment vectors	29
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation	28
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning	28
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling	28
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES	27
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping	26
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics†	26
Using GANs with adaptive training data to search for new molecules	26
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection	25
SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors	25
HobPre: accurate prediction of human oral bioavailability for small molecules	25
Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions	25
Deep scaffold hopping with multimodal transformer neural networks	24
DockStream: a docking wrapper to enhance de novo molecular design	24
Industry-scale application and evaluation of deep learning for drug target prediction	24
STOUT: SMILES to IUPAC names using neural machine translation	23
GEN: highly efficient SMILES explorer using autodidactic generative examination networks	23
SANCDB: an update on South African natural compounds and their readily available analogs	23
Using informative features in machine learning based method for COVID-19 drug repurposing	21
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network	21
MAIP: a web service for predicting blood‐stage malaria inhibitors	20
Predicting in silico electron ionization mass spectra using quantum chemistry	20
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform	20
Sequence-based prediction of protein binding regions and drug–target interactions	19
The diatomic molecular spectroscopy database	19
Transformer-based molecular optimization beyond matched molecular pairs	19
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration	19
MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning	18
Too sweet: cheminformatics for deglycosylation in natural products	18
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles	17
Uncertainty-aware prediction of chemical reaction yields with graph neural networks	17
Designing optimized drug candidates with Generative Adversarial Network	17

FAIR chemical structures in the Journal of Cheminformatics	17
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling	17
The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction	17
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges	16
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates	16
KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development	16
Predicting liver cytosol stability of small molecules	16
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach	15
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification	15
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	14
The effect of noise on the predictive limit of QSAR models	14
Splitting chemical structure data sets for federated privacy-preserving machine learning	14
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction	14
Assessing the information content of structural and protein–ligand interaction representations for the classification of kinase inhibitor binding modes via machine learning and active learning	14
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer	14
LEADD: Lamarckian evolutionary algorithm for de novo drug design	14
A fingerprints based molecular property prediction method using the BERT model	13
Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses	13
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19	13
Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning	13
DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions	13
Multi-PLI: interpretable multi‐task deep learning model for unifying protein–ligand interaction datasets	13
MolData, a molecular benchmark for disease and target based machine learning	13
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting	12
Human-in-the-loop assisted de novo molecular design	12
Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models	12
Substructure-based neural machine translation for retrosynthetic prediction	12
Papyrus: a large-scale curated dataset aimed at bioactivity predictions	12
“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool	12
Blood–brain barrier penetration prediction enhanced by uncertainty estimation	12
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning	12
Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds	12
MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry	12