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 HIV 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.

Select a protein structure: [switch to full structure list] HIV  SIV
	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: