ArticleBioinformatics (Oxford, England)2019
Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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74 citing papers in PubMed.
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- Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms.Chemical reviews · 2026Review
- Two faces of drug repurposing data in machine learning-driven structure-based virtual screening supported by interaction fingerprints.Journal of computer-aided molecular design · 2026Article
- Structure-aware artificial intelligence for next-generation drug discovery: from protein-ligand modeling to generative biomolecular design.Briefings in bioinformatics · 2026Review
- Structural Knowledge Is What Matters in Protein-Ligand Binding Affinity Prediction.Molecules (Basel, Switzerland) · 2026Article
- Reindeer: a protein-ligand feature generator software for machine learning algorithms.BMC bioinformatics · 2026Article
- PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.International journal of molecular sciences · 2026Article
- Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structures.Briefings in bioinformatics · 2026Article
- A geometric graph-based deep learning model for drug-target affinity prediction.BMC bioinformatics · 2025Article
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- Integrating Machine Learning into Free Energy Perturbation Workflows.Journal of chemical information and modeling · 2025Review
- HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors.Journal of cheminformatics · 2025Article
- MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.Nature communications · 2025Article
- Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.PLoS computational biology · 2025Article
- Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World.Chemical research in toxicology · 2025Review
- A Database for Large-Scale Docking and Experimental Results.Journal of chemical information and modeling · 2025Article
- Instruction multi-constraint molecular generation using a teacher-student large language model.BMC biology · 2025Article
14 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
motivationFingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the overall FP abundance, only a few FPs represent the 3D structure of the molecule, and hardly any encode protein-ligand interactions.
resultsHere, we present a Protein-Ligand Extended Connectivity (PLEC) FP that implicitly encodes protein-ligand interactions by pairing the ECFP environments from the ligand and the protein. PLEC FPs were used to construct different machine learning models tailored for predicting protein-ligand affinities (pKi∕d). Even the simplest linear model built on the PLEC FP achieved Rp = 0.817 on the Protein Databank (PDB) bind v2016 'core set', demonstrating its descriptive power. AVAILABILITY AND IMPLEMENTATION: The PLEC FP has been implemented in the Open Drug Discovery Toolkit (https://github.com/oddt/oddt). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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