Journal of Cheminformatics

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
Memory-assisted reinforcement learning for diverse molecular de novo design	61
FP-ADMET: a compendium of fingerprint-based ADMET prediction models	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
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
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
Designing optimized drug candidates with Generative Adversarial Network	39
Using GANs with adaptive training data to search for new molecules	37
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids	36
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES	36

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
HobPre: accurate prediction of human oral bioavailability for small molecules	35
A fingerprints based molecular property prediction method using the BERT model	34
Learning protein-ligand binding affinity with atomic environment vectors	34
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
Benchmarks for interpretation of QSAR models	33
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection	32
DockStream: a docking wrapper to enhance de novo molecular design	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
Sequence-based prediction of protein binding regions and drug–target interactions	27
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
SANCDB: an update on South African natural compounds and their readily available analogs	26
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach	26
The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction	25
Transformer-based molecular optimization beyond matched molecular pairs	25
MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning	25
Explainable uncertainty quantifications for deep learning-based molecular property prediction	24
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning	23
STOUT: SMILES to IUPAC names using neural machine translation	23
Splitting chemical structure data sets for federated privacy-preserving machine learning	23
Uncertainty-aware prediction of chemical reaction yields with graph neural networks	23
Using informative features in machine learning based method for COVID-19 drug repurposing	22
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
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes	21
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
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
Too sweet: cheminformatics for deglycosylation in natural products	20
LEADD: Lamarckian evolutionary algorithm for de novo drug design	20
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
FAIR chemical structures in the Journal of Cheminformatics	19
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation	18
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations	18
Blood–brain barrier penetration prediction enhanced by uncertainty estimation	17
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
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

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
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges	15
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
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
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19	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
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation	14
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
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
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
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials	12
A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data	11
Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles	11
A multitask GNN-based interpretable model for discovery of selective JAK inhibitors	11
Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity	11
Visualizing chemical space networks with RDKit and NetworkX	11
Review of techniques and models used in optical chemical structure recognition in images and scanned documents	11
QPHAR: quantitative pharmacophore activity relationship: method and validation	11
ChemSpectra: a web-based spectra editor for analytical data	11
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions	10
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules	10
Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence	10
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data	10
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering	10
FPocketWeb: protein pocket hunting in a web browser	10
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson	10
Surge: a fast open-source chemical graph generator	10
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty	10
Deep learning integration of molecular and interactome data for protein–compound interaction prediction	10
DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning	10
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models	10
Machine intelligence-driven framework for optimized hit selection in virtual screening	10
MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle	10
canSAR chemistry registration and standardization pipeline	10
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores	10
How to approach machine learning-based prediction of drug/compound–target interactions	9
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping	9
ChemProps: A RESTful API enabled database for composite polymer name standardization	9
DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data	9
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis	9
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction	9
Processing binding data using an open-source workflow	9
Flame: an open source framework for model development, hosting, and usage in production environments	9
Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules	9
HD_BPMDS: a curated binary pattern multitarget dataset of Huntington’s disease–targeting agents	9
Harnessing Shannon entropy-based descriptors in machine learning models to enhance the prediction accuracy of molecular properties	8
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets	8
What makes a reaction network “chemical”?	8
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions	8
InflamNat: web-based database and predictor of anti-inflammatory natural products	8
Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier	8
DeepAR: a novel deep learning-based hybrid framework for the interpretable prediction of androgen receptor antagonists	8
Charged aerosol detector response modeling for fatty acids based on experimental settings and molecular features: a machine learning approach	8
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products	8
LigninGraphs: lignin structure determination with multiscale graph modeling	8
A machine learning platform for the discovery of materials	8

ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks	8
DECIMER—hand-drawn molecule images dataset	8
TB-IECS: an accurate machine learning-based scoring function for virtual screening	8
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients	8
Reconstruction of lossless molecular representations from fingerprints	7
Investigation of chemical structure recognition by encoder–decoder models in learning progress	7
PIKAChU: a Python-based informatics kit for analysing chemical units	7
Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach	7
Advancing material property prediction: using physics-informed machine learning models for viscosity	7
Force field-inspired molecular representation learning for property prediction	7
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation	7
NMR shift prediction from small data quantities	7
OWSum: algorithmic odor prediction and insight into structure-odor relationships	7
Explaining and avoiding failure modes in goal-directed generation of small molecules	7
Development of a chemogenomics library for phenotypic screening	7
Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison	7
PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow	7
In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network	7
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules	7
Chemical reaction network knowledge graphs: the OntoRXN ontology	6
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data	6
Effectiveness of molecular fingerprints for exploring the chemical space of natural products	6
Hybrid semantic recommender system for chemical compounds in large-scale datasets	6
DeepSA: a deep-learning driven predictor of compound synthesis accessibility	6
Application of deep metric learning to molecular graph similarity	6
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data	6
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification	6
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures	6
Double-head transformer neural network for molecular property prediction	6
Diversifying cheminformatics	6
Improving VAE based molecular representations for compound property prediction	6
Integrating synthetic accessibility with AI-based generative drug design	6
Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models	6
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling	5
SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches	5
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states	5
Cobdock: an accurate and practical machine learning-based consensus blind docking method	5
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES	5
Extended study on atomic featurization in graph neural networks for molecular property prediction	5
MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal–organic frameworks utilizing graph convolutional networks	5
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on “drug-target-pathway” heterogenous network	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
DrugTax: package for drug taxonomy identification and explainable feature extraction	5
RanDepict: Random chemical structure depiction generator	5
Using Jupyter Notebooks for re-training machine learning models	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
Global reactivity models are impactful in industrial synthesis applications	5
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis	5
Machine learning for identification of silylated derivatives from mass spectra	5
RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking	5
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods	5
Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs	5
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease	4
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop	4
Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors	4
LinChemIn: SynGraph—a data model and a toolkit to analyze and compare synthetic routes	4
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences	4
Ensemble completeness in conformer sampling: the case of small macrocycles	4
Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors	4
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction	4
Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions	4
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions	4
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network	4
LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP	4
ProfhEX: AI-based platform for small molecules liability profiling	4
Probabilistic generative transformer language models for generative design of molecules	4
Art driven by visual representations of chemical space	4
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond	4
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools	4
Adaptive language model training for molecular design	4
HybridGCN for protein solubility prediction with adaptive weighting of multiple features	4
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons	4