Protein Feature Accent

Purpose: To view 3D structures of HIV proteins and to map a desired sequence (e.g., short functional domain or epitope) directly onto the interactive graphic.

How to use: Click on one of the structures listed, or upload a structure file in PDB format. Uploading a sequence is not required. Any sequences you do provide will be analyzed for entropy and glycosylation, aligned with the structure sequence, and displayed. For details, see Protein Feature Accent Explanation. This tool requires that Java be installed on your computer.

Click here for a list of all the HCV structures available.

This is a beta version!
Some capabilities are not fully implemented, and there may be bugs or other problems. Please use with care and a sense of humor.

Java and Javascript required This tool uses a Java applet that depends upon javascript for all of its interactive features. If you have javascript disabled in your browser, you may see a protein structure, but none of the interactive features of this tool will function. The menu of available structures below will not load with javascript turned off, but you may still be able to upload a PDB file.

Select a protein structure: [switch to full structure list]
	OR
upload a PDB file:
You may provide an amino acid sequence alignment (or a single unaligned sequence) below:
Paste your sequence(s) here [Sample Input]
or upload a sequence file:

References:

Jmol website

Contributors:

Bette Korber - concept, vision, and leadership (at lanl.gov, email address 'btk')
S. 'Gnana' Gnanakaran - concept, structures information (at lanl.gov, email address 'gnana')
Jim Thurmond - programming and design

Tool Development Sponsored In Part By:

Comprehensive Antibody-Vaccine Immune Monitoring Consortium

Questions or comments? Contact us at hcv-info@lanl.gov