ArticleJournal of cheminformatics2014
A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening.
Article in Journal of cheminformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- AI-Assisted Protein-Peptide Complex Prediction in a Practical Setting.Journal of computational chemistry · 2025Article
- Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins.ACS omega · 2022Article
- Artificial intelligence and machine learning-aided drug discovery in central nervous system diseases: State-of-the-arts and future directions.Medicinal research reviews · 2021Review
- Prediction of Premature Termination Codon Suppressing Compounds for Treatment of Duchenne Muscular Dystrophy Using Machine Learning.Molecules (Basel, Switzerland) · 2020Article
- Chemoinformatics and structural bioinformatics in OCaml.Journal of cheminformatics · 2019Article
- Development and Testing of Druglike Screening Libraries.Journal of chemical information and modeling · 2019Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015.Journal of computer-aided molecular design · 2016Article
- Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout.Journal of computer-aided molecular design · 2016Article
- MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites.Frontiers in pharmacology · 2016Article
- BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.Journal of cheminformatics · 2016Article
- Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors.Journal of molecular modeling · 2015Article
- Hierarchical virtual screening approaches in small molecule drug discovery.Methods (San Diego, Calif.) · 2015Review
- ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation.Journal of cheminformatics · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMeasures of similarity for chemical molecules have been developed since the dawn of chemoinformatics. Molecular similarity has been measured by a variety of methods including molecular descriptor based similarity, common molecular fragments, graph matching and 3D methods such as shape matching. Similarity measures are widespread in practice and have proven to be useful in drug discovery. Because of our interest in electrostatics and high throughput ligand-based virtual screening, we sought to exploit the information contained in atomic coordinates and partial charges of a molecule.
resultsA new molecular descriptor based on partial charges is proposed. It uses the autocorrelation function and linear binning to encode all atoms of a molecule into two rotation-translation invariant vectors. Combined with a scoring function, the descriptor allows to rank-order a database of compounds versus a query molecule. The proposed implementation is called ACPC (AutoCorrelation of Partial Charges) and released in open source. Extensive retrospective ligand-based virtual screening experiments were performed and other methods were compared with in order to validate the method and associated protocol.
conclusionsWhile it is a simple method, it performed remarkably well in experiments. At an average speed of 1649 molecules per second, it reached an average median area under the curve of 0.81 on 40 different targets; hence validating the proposed protocol and implementation.
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