Part VII: Using VAST+ to find structural homologs

Instructions:

1. We will use the VAST+ program to find homologs of the SARS-CoV2 Spike Protein

(PDB ID 6VXX). Go to https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi and

enter 6VXX for the PDB ID. The NCBI structural citation for this PDB file will come up.

For one of these hits, click the little "+" box near the PDB ID. Click Visualize 3D

Structure Superposition and then iCn3D.

2.

3. Take a look at some of the tools for analysis and visualization. You can learn quite a bit

about the relationship between the aligned structures using these tools.

4. Go back to your search and use the filters to find a match around 80% identity, and one

with around 30% identity.

5. Save a picture of each of your superimposed alignments. To do this go to Style then set

the background to white. Then click the little camera (or go File to Save File to iCn3D

PNG image). Paste the image inline into this homework.

Questions:

1. What were the name, sequence identity, and RMSD of each of the hits you chose?

2. How did they differ both in terms of sequence and in terms of structure?

3. Is there anything special about the regions of the protein that have weaker structural

alignment?

4. How might a tool like this be used to learn something about the coronavirus?

5. Why is structural alignment different from sequence alignment and why might it be

useful?

6. Starting with this page:

https://www.ncbi.nlm.nih.gov/Structure/vastplus/docs/vastplus_help.html, do some

research and explain how does VAST+ works (in your own words, do not copy and paste

anything!).