Record Details

EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.

DIR@IMTECH: CSIR-Institute of Microbial Technology

View Archive Info
 
 
Field Value
 
Title EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.
 
Creator Loharch, Saurabh
Bhutani, Isha
Jain, Kamal
Gupta, Pawan
Sahoo, Debendra K
Parkesh, Raman
 
Subject QR Microbiology
 
Description 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.
 
Publisher Oxford University Press
 
Date 2015
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/1655/1/Raman%20Prakesh%202015%20%20Database-2015-Loharch-database_bav013.pdf
Loharch, Saurabh and Bhutani, Isha and Jain, Kamal and Gupta, Pawan and Sahoo, Debendra K and Parkesh, Raman (2015) EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database : the journal of biological databases and curation, 2015. ISSN 1758-0463
 
Relation http://database.oxfordjournals.org/content/2015/bav013.long
http://crdd.osdd.net/open/1655/