TY - JOUR
T1 - VnD
T2 - A structure-centric database of disease-related SNPs and drugs
AU - Yang, Jin Ok
AU - Oh, Sangho
AU - Ko, Gunhwan
AU - Park, Seong Jin
AU - Kim, Woo Yeon
AU - Lee, Byungwook
AU - Lee, Sanghyuk
N1 - Funding Information:
Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program and ‘Systems Biology Infrastructure Establishment Grant’ provided by Gwangju Institute of Science & Technology in 2010 through Ewha Research Center for Systems Biology (ERCSB). Funding for open access charge: KRIBB Research Initiative Program.
PY - 2011/1
Y1 - 2011/1
N2 - 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 diseaserelated 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 drugrelated 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.
AB - 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 diseaserelated 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 drugrelated 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.
UR - http://www.scopus.com/inward/record.url?scp=78651321208&partnerID=8YFLogxK
U2 - 10.1093/nar/gkq957
DO - 10.1093/nar/gkq957
M3 - Article
C2 - 21051351
AN - SCOPUS:78651321208
SN - 0305-1048
VL - 39
SP - D939-D944
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -