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Database Commons - VnD

VnD

Citations: 7

z-index 0.00

Short name VnD
Full name Variations and Drugs
Description VnD is a structure-centric database of disease-related SNPs and drugs.
URL http://vnd.kobic.re.kr:8080/VnD/
Year founded 2010
Last update & version 2010-11-04    v1.0
Availability Free to all users
University/Institution hosted Korea Research Institute of Bioscience and Biotechnology
Address 111 Gwahangno,Yuseong-gu,Daejeon 305Ð806,Korea
City Daejeon
Province/State
Country/Region Korea Rep.
Contact name Byungwook Lee
Contact email bulee@kribb.re.kr
Data type(s)
Major organism(s)
Keyword(s)
  • drug
  • SNP
Publication(s)
  • VnD: a structure-centric database of disease-related SNPs and drugs. [PMID: 21051351]

    Jin Ok Yang, Sangho Oh, Gunhwan Ko, Seong-Jin Park, Woo-Yeon Kim, Byungwook Lee, Sanghyuk Lee
    Nucleic acids research 2011:39(Database issue)
    7 Citations (Google Scholar as of 2016-05-04)

    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.

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Tags

Disease DNA
Homo sapiens
drug SNP

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Hongyan Yin [2016-03-31]
    • Mengwei Li [2016-02-15]
    • Hongyan Yin [2015-11-22]
    • Hongyan Yin [2015-06-26]
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