Journal of Cheminformatics

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 2021-09-01 to 2025-09-01.)
ArticleCitations
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision239
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder110
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands88
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding88
Generating diversity and securing completeness in algorithmic retrosynthesis82
Assessing interaction recovery of predicted protein-ligand poses74
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning68
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification67
Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients65
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors65
Explainable uncertainty quantifications for deep learning-based molecular property prediction58
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials58
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint57
Transformer-based molecular optimization beyond matched molecular pairs57
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph51
Paths to cheminformatics: Q&A with Ann M. Richard51
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data48
Deep learning of multimodal networks with topological regularization for drug repositioning46
AdapTor: Adaptive Topological Regression for quantitative structure–activity relationship modeling46
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action46
APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions45
VSFlow: an open-source ligand-based virtual screening tool44
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery41
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features41
PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions41
One chiral fingerprint to find them all40
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding39
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry38
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application38
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction36
Implementation of an open chemistry knowledge base with a Semantic Wiki36
Explaining compound activity predictions with a substructure-aware loss for graph neural networks34
Crossover operators for molecular graphs with an application to virtual drug screening34
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