Journal of Cheminformatics

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
An open source chemical structure curation pipeline using RDKit	157
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome	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
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map	55
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra	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
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors	34
spyrmsd: symmetry-corrected RMSD calculations in Python	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
Benchmarks for interpretation of QSAR models	30
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
Learning protein-ligand binding affinity with atomic environment vectors	29
InChI version 1.06: now more than 99.99% reliable	29
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling	28
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
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES	27
Using GANs with adaptive training data to search for new molecules	26
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
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
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform	20
MAIP: a web service for predicting blood‐stage malaria inhibitors	20
Predicting in silico electron ionization mass spectra using quantum chemistry	20
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration	19
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
Too sweet: cheminformatics for deglycosylation in natural products	18
MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning	18
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
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
Predicting liver cytosol stability of small molecules	16
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
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
LEADD: Lamarckian evolutionary algorithm for de novo drug design	14
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
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
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
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
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
Development and evaluation of two-parameter linear free energy models for the prediction of human skin permeability coefficient of neutral organic chemicals	11
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial	11
Explainable uncertainty quantifications for deep learning-based molecular property prediction	11
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds	11
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding	11
Compressed graph representation for scalable molecular graph generation	11
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data	11
Nonadditivity in public and inhouse data: implications for drug design	11
Activity landscape image analysis using convolutional neural networks	11
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors	10
Probabilistic metabolite annotation using retention time prediction and meta-learned projections	10
MetaRF: attention-based random forest for reaction yield prediction with a few trails	10
BitterMatch: recommendation systems for matching molecules with bitter taste receptors	10
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics	10
IDSM ChemWebRDF: SPARQLing small-molecule datasets	10
RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions	10
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	10
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data	10
A multitask GNN-based interpretable model for discovery of selective JAK inhibitors	10
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning	10
Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles	10
Molecular generation by Fast Assembly of (Deep)SMILES fragments	9
Deep generative model for drug design from protein target sequence	9
Machine intelligence-driven framework for optimized hit selection in virtual screening	9
Assessing the calibration in toxicological in vitro models with conformal prediction	9
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features	9
Surge: a fast open-source chemical graph generator	9
DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature	9
Improving the performance of models for one-step retrosynthesis through re-ranking	9
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty	8
Flame: an open source framework for model development, hosting, and usage in production environments	8
Charged aerosol detector response modeling for fatty acids based on experimental settings and molecular features: a machine learning approach	8
Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity	8
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions	8
A machine learning platform for the discovery of materials	8
Deep learning integration of molecular and interactome data for protein–compound interaction prediction	8
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	8
QPHAR: quantitative pharmacophore activity relationship: method and validation	8
ChemSpectra: a web-based spectra editor for analytical data	8
Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning	8
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature	8
What makes a reaction network “chemical”?	8
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models	8
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	7
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products	7
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine	7
MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle	7

DECIMER—hand-drawn molecule images dataset	7
ChemProps: A RESTful API enabled database for composite polymer name standardization	7
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	7
Systemic evolutionary chemical space exploration for drug discovery	7
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	7
Exploring QSAR models for activity-cliff prediction	7
Processing binding data using an open-source workflow	7
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization	6
FPocketWeb: protein pocket hunting in a web browser	6
Hybrid semantic recommender system for chemical compounds in large-scale datasets	6
Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier	6
Diversifying cheminformatics	6
Review of techniques and models used in optical chemical structure recognition in images and scanned documents	6
UnCorrupt SMILES: a novel approach to de novo design	6
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning	6
Investigation of chemical structure recognition by encoder–decoder models in learning progress	6
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation	6
LigninGraphs: lignin structure determination with multiscale graph modeling	6
ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction	6
DFFNDDS: prediction of synergistic drug combinations with dual feature fusion networks	6
Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules	5
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis	5
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	5
DeepAR: a novel deep learning-based hybrid framework for the interpretable prediction of androgen receptor antagonists	5
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	5
Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison	5
PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow	5
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions	5
ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding	5
Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization	5
SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides	5
In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network	5
PIKAChU: a Python-based informatics kit for analysing chemical units	5
Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach	5
A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data	5
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	5
rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization	5
Reconstruction of lossless molecular representations from fingerprints	5
OWSum: algorithmic odor prediction and insight into structure-odor relationships	5
canSAR chemistry registration and standardization pipeline	5
Application of deep metric learning to molecular graph similarity	4
MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation	4
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering	4
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	4
Neural machine translation of chemical nomenclature between English and Chinese	4
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	4
Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence	4
Using Jupyter Notebooks for re-training machine learning models	4
Development of a chemogenomics library for phenotypic screening	4
How to approach machine learning-based prediction of drug/compound–target interactions	4
Visualizing chemical space networks with RDKit and NetworkX	4
Ensemble completeness in conformer sampling: the case of small macrocycles	4
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons	4
InflamNat: web-based database and predictor of anti-inflammatory natural products	4
Force field-inspired molecular representation learning for property prediction	4
NMR shift prediction from small data quantities	4
Global reactivity models are impactful in industrial synthesis applications	4
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states	4
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules	4
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES	4