ArticleBMC bioinformatics2015
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Examining Genetic Variants Associated with FOXP1 Syndrome through Molecular Dynamics of Its DNA-Binding Domain and Self-Organizing Maps.Journal of chemical information and modeling · 2026Article
- Novel cyclic heptapeptides as potential therapeutics against methicillin-resistant Staphylococcus aureus infections.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Tranylcypromine: a promising repurposed drug against Leishmaniases.Frontiers in microbiology · 2025Article
- Computational proteomics analysis ofFrontiers in plant science · 2024Article
- Phytotherapeutic potential ofIn silico pharmacology · 2024Article
- The artificial neural network selects saccharides from natural sources a promise for potential FimH inhibitor to prevent UTI infections.In silico pharmacology · 2024Article
- TCDD-Induced Allosteric Perturbation of the AhR:ARNT Binding to DNA.International journal of molecular sciences · 2023Article
- Evaluating Biofilm Inhibitory Potential in Fish Pathogen,Antibiotics (Basel, Switzerland) · 2023Article
- Discovery of new potent lysine specific histone demythelase-1 inhibitors (LSD-1) using structure based and ligand based molecular modelling and machine learning.RSC advances · 2022Article
- PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations.Journal of chemical theory and computation · 2022Article
- Peptibody Based on FGFR1-Binding Peptides From the FGF4 Sequence as a Cancer-Targeting Agent.Frontiers in pharmacology · 2021Article
- The PEG-responding desiccome of the alder microsymbiont Frankia alni.Scientific reports · 2018Article
- Leishmania infantum 5'-Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target.BMC structural biology · 2017Article
- ADME-Space: a new tool for medicinal chemists to explore ADME properties.Scientific reports · 2017Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentifying druggable cavities on a protein surface is a crucial step in structure based drug design. The cavities have to present suitable size and shape, as well as appropriate chemical complementarity with ligands.
resultsWe present a novel cavity prediction method that analyzes results of virtual screening of specific ligands or fragment libraries by means of Self-Organizing Maps. We demonstrate the method with two thoroughly studied proteins where it successfully identified their active sites (AS) and relevant secondary binding sites (BS). Moreover, known active ligands mapped the AS better than inactive ones. Interestingly, docking a naive fragment library brought even more insight. We then systematically applied the method to the 102 targets from the DUD-E database, where it showed a 90% identification rate of the AS among the first three consensual clusters of the SOM, and in 82% of the cases as the first one. Further analysis by chemical decomposition of the fragments improved BS prediction. Chemical substructures that are representative of the active ligands preferentially mapped in the AS.
conclusionThe new approach provides valuable information both on relevant BSs and on chemical features promoting bioactivity.
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