ArticleDatabase : the journal of biological databases and curation2015
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Enhancing anti-tumor immune responses through combination therapies: epigenetic drugs and immune checkpoint inhibitors.Frontiers in immunology · 2023Review
- SMART v1.0: A Database for Small Molecules with Functional Implications in Plants.Interdisciplinary sciences, computational life sciences · 2022Article
- A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma.Frontiers in cell and developmental biology · 2021Article
- Recent progress on cheminformatics approaches to epigenetic drug discovery.Drug discovery today · 2020Review
- FlavoDb: a web-based chemical repository of flavonoid compounds.3 Biotech · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed EpiDBase (www.epidbase.org), an interactive database of small molecule ligands of epigenetic protein families by bringing together experimental, structural and chemoinformatic data in one place. Currently, EpiDBase encompasses 5784 unique ligands (11 422 entries) of various epigenetic markers such as writers, erasers and readers. The EpiDBase includes experimental IC(50) values, ligand molecular weight, hydrogen bond donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings, InChIKey, two-dimensional and three-dimensional (3D) chemical structures. A catalog of all epidbase ligands based on the molecular weight is also provided. A structure editor is provided for 3D visualization of ligands. EpiDBase is integrated with tools like text search, disease-specific search, advanced search, substructure, and similarity analysis. Advanced analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. The EpiDBase is curated to identify unique molecular scaffolds. Initially, molecules were selected by removing peptides, macrocycles and other complex structures and then processed for conformational sampling by generating 3D conformers. Subsequent filtering through Zinc Is Not Commercial (ZINC: a free database of commercially available compounds for virtual screening) and Lilly MedChem regular rules retained many distinctive drug-like molecules. These molecules were then analyzed for physicochemical properties using OpenBabel descriptors and clustered using various methods such as hierarchical clustering, binning partition and multidimensional scaling. EpiDBase provides comprehensive resources for further design, development and refinement of small molecule modulators of epigenetic markers.
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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.