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

Database : the Journal of Biological Databases and Curation
Saurabh LoharchRaman Parkesh

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 th...Continue Reading

References

Dec 1, 1965·Biopolymers·W L Koltun
Feb 19, 2000·Journal of Molecular Graphics & Modelling·D J Wild, C J Blankley
Mar 4, 2003·Nature Reviews. Drug Discovery·Han van de Waterbeemd, Eric Gifford
May 2, 2003·Annals of the New York Academy of Sciences·Thea Kalebic
Jan 26, 2005·Journal of Chemical Information and Modeling·John J Irwin, Brian K Shoichet
Aug 7, 2007·Toxicological Sciences : an Official Journal of the Society of Toxicology·Moshe Szyf
Nov 8, 2007·Journal of Chemical Information and Modeling·Tiejun ChengLuhua Lai
Mar 11, 2008·Chemistry Central Journal·Noel M O'BoyleGeoffrey R Hutchison
Feb 18, 2010·Journal of Medicinal Chemistry·Anthony NichollsBrian Kelley
Nov 16, 2010·Nucleic Acids Research·Ian M FingermanGregory D Schuler
May 18, 2011·Nucleic Acids Research·Tyler W H BackmanThomas Girke
Sep 29, 2011·Nucleic Acids Research·Anna GaultonJohn P Overington
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Jan 5, 2012·Nature Reviews. Genetics·Robert Feil, Mario F Fraga
Apr 14, 2012·Nature Reviews. Drug Discovery·Cheryl H ArrowsmithMatthieu Schapira
Apr 27, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Lirong PeiHuidong Shi
Jun 22, 2012·Bioinformatics·Lihua LiuMatthieu Schapira
Jun 23, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Robert S Lahue, Aisling Frizzell
Aug 17, 2012·The New England Journal of Medicine·Mark A DawsonBrian J P Huntly
Oct 16, 2012·Journal of Medicinal Chemistry·Robert F Bruns, Ian A Watson
Nov 2, 2012·The New England Journal of Medicine·Margit Rosner, Markus Hengstschläger
Nov 30, 2012·Nucleic Acids Research·Ian M FingermanGregory D Schuler
Dec 6, 2012·Nature Structural & Molecular Biology·Catherine A MusselmanTatiana G Kutateladze
Jan 25, 2013·Journal of Cheminformatics·Stephen HellerIgor Pletnev
Oct 29, 2013·Nucleic Acids Research·Ankita MehtaRaman Parkesh
Jan 29, 2014·Bioinformatics·Jamel MeslamaniMing-Ming Zhou
Nov 8, 2012·ACS Medicinal Chemistry Letters·Gerard Rosse

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Citations

Jan 23, 2016·Journal of Medicinal Chemistry·Vineet Pande
Nov 9, 2019·Future Medicinal Chemistry·Saurabh Loharch, Raman Parkesh
Nov 7, 2019·3 Biotech·Baban S KolteRohan J Meshram
Mar 27, 2021·Journal of Medicinal Chemistry·Norberto Sánchez-Cruz, José L Medina-Franco
May 11, 2021·Frontiers in Cell and Developmental Biology·Aleksandar KrsticDavid J Duffy
Oct 15, 2021·Interdisciplinary Sciences, Computational Life Sciences·Beilei LeiChuang Ma

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Methods Mentioned

BETA
MDS
X-ray

Software Mentioned

Universal Force Field ( UFF
Google scholar
ChemDiff
js
MDS
Vlife2Draw
ChemAxon Standraizer
Mol2
MMFF
ChemBioDraw Ultra

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