Protein Feature Accent

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.

Purpose:   The Protein Feature Accent tool is a quick way to map protein sequence features (for example a short functional domain or an epitope) from a sequence directly on to an interactive graphic of the corresponding 3-D structure of the protein.

How to use:   The tool needs only to be directed to use a particular protein structure file in PDB format. Uploading a sequence is not required; the sequence associated with the chosen structure will always be displayed. Any sequences you do provide will be analyzed (for entropy, etc.), aligned with the structure sequence, and displayed.
Selected HIV Env structures are provided in a menu below. More proteins and structures will soon be made available this way as well. If you prefer, you may upload a PDB file for a structure you wish to use instead of those available here.

New features:

• Predicted N-linked glycosylation site highlighting
• User-supplied alignment entropy color scheme
• PDB file upload option

We are in the process of adding additional features to the tool.

Select a structure:	1G9M: HXBC2 gp120 1RZK: YU2 gp120 2B4C: JRFL gp120 2BF1: MAC32H gp120 2NY7: HXBC2 gp120
	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 (at lanl.gov, email address 'thurmond')

Tool Development Sponsored In Part By: