Methods & Guides
Workflow of VnD
- A) Keyword Search : VnD provides four search interfaces using protein, gene, SNP, and disease keywords.
- - Protein search : Uniprot or PDB ID
- - Gene search : Gene symbol
- - SNP search : dbSNP ID (rs number)
- - Disease search : Disease term
- B) Sequence Search: VnD provides a sequence homology search interface.
- - Sequence homology search: user queried protein sequences
- C) Structure Analysis: the VnD web site provides an analysis tool for analyzing structural changes resulting
fromamino acid changes in a protein sequence.
- - Protein structural Analysis: user queried protein sequences and amino acid change
- - Options: [queried protein sequences] [position],[ref_aa],[mutant_aa]
- - This pipeline provides protein physico-chemical properties and pocket sizes
Protein Structure Analysis
(wild-type and mutants)
The protein structure analysis page includes variation structure analysis and target/ligand information. Protein structure, distance values between SNP and Pockets, and docking information of ligands are provided via the "Variation Structure Analysis" table. When you click the "view" link, a page is displayed to visualize the protein structure with a docked ligand using Chime software. You must install Chime software to show the protein structure on your local machine.
Gene, Protein and
This page includes gene, protein, and disease information. When you click on the number link in the "No. of SNPs" column, you can see a list of SNPs associated with the gene. Clicking the icon will take you to the "Variation Structure Analysis" section,. The disease information was obtained from GAD and OMIM databases.