ProteinScope

Free viewer for RCSB Protein Data Bank* files

Register

Feedback

Home

- Make sure you have the latest drivers installed for your video card for optimum performance of all your 3D applications.
- Install the latest version of the Direct X 8.1 runtime, available here.
- Set your display properties to 32 bits per pixel.
- If you are having difficulty please send an email describing the problem.
- ProteinScope and proteinscope.com are regularly updated so check back here frequently.

The motif highlight feature of ProteinScope allows users to illuminate binding sites and other areas of interest within a protein as long as the amino acid sequence of the region is known. Identity sequences extracted from various motif databases are supported, the example here was done using PROSITE as a starting point..

Visual pigments (opsins) retinal binding site.

- From the PROSITE entry for this motif, scroll to the bottom heading "Retrieve an alignment of SWISS-PROT true positive hits". 
- Click on "FASTA format". Select and copy into the clipboard a sequence, here VSylfAKSNTvyNPviY is chosen.
- Open the Protein Data Bank FASTA search page, paste the sequence into the FASTA box. Click the Search button
- On the results page, select the third entry, 1KPX, by clicking the alignment link. The FASTA results page will open.
- Select the sequence within the protein that corresponds to the search sequence, LPAYFAKSATIYNPVIY put in clipboard.
- Launch ProteinScope. Select File/Open from RCSB... enter 1KPX and hit return. The PDB file will load over the internet. 
- Select View/Highlight Motif, paste in the sequence from the clipboard, and hit See It! Rotate and zoom to observe motif.

*Citations: H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). All trademarks used here property of their respective owners.

ProteinScope® © Mark S. Morris 2002 - 2019
All rights reserved.