VnD : a structure-centric database of disease-related SNPs and drugs

Cited 9 time in scopus
Metadata Downloads
Title
VnD : a structure-centric database of disease-related SNPs and drugs
Author(s)
Jin Ok Yang; Sang Ho Oh; Kun Hwan GoSeongjin Park; W Y Kim; ByungUk Lee; Sanghyuk Lee
Bibliographic Citation
Nucleic Acids Research, vol. 39, no. D, pp. D939-D944
Publication Year
2011
Abstract
Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkq957
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
Files in This Item:

Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.