ArticleMedChemComm2019
Binding site characterization - similarity, promiscuity, and druggability.
Article in MedChemComm, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The trial behind it
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Who cites it
13 citing papers in PubMed.
- Computer-Aided Discovery of Drugs Against Chagas Disease.Methods in molecular biology (Clifton, N.J.) · 2026Article
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- Article
- TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa.Journal of computer-aided molecular design · 2023Article
- TWN-RENCOD: A novel method for protein binding site comparison.Computational and structural biotechnology journal · 2023Article
- Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.Journal of chemical information and modeling · 2022Article
- New Drug Design Avenues Targeting Alzheimer's Disease by Pharmacoinformatics-Aided Tools.Pharmaceutics · 2022Review
- Common Structural Pattern for Flecainide Binding in Atrial-Selective KPharmaceutics · 2022Article
- Editorial: Chemoinformatics Approaches to Structure- and Ligand-Based Drug Design, Volume II.Frontiers in pharmacology · 2022Article
- Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace.Briefings in bioinformatics · 2021Review
- An up-to-date overview of computational polypharmacology in modern drug discovery.Expert opinion on drug discovery · 2020Review
- Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike.Computational and structural biotechnology journal · 2020Article
- Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The elucidation of non-obvious binding site similarities has provided useful indications for the establishment of polypharmacology, the identification of potential off-targets, or the repurposing of known drugs. The concept underlying all of these approaches is promiscuous binding which can be analyzed from a ligand-based or a binding site-based perspective. Herein, we applied methods for the automated analysis and comparison of protein binding sites to study promiscuous binding on a novel dataset of sites in complex with ligands sharing common shape and physicochemical properties. We show the suitability of this dataset for the benchmarking of novel binding site comparison methods. Our investigations also reveal promising directions for further in-depth analyses of promiscuity and druggability in a pocket-centered manner. Drawbacks concerning binding site similarity assessment and druggability prediction are outlined, enabling researchers to avoid the typical pitfalls of binding site analyses.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.