FUGUE: Sequence-structure homology recognition


15 Apr 2015
FUGUE has changed its URL. Please bookmark http://mizuguchilab.org/fugue/.
16 Apr 2007
A bug has been fixed in the alignment server. Uploading a PDB file now works properly.
7 Mar 2007 (IMPORTANT)
A new alignment server available.
13 Dec 2006 (IMPORTANT)
A new temporary server (homology search) available.
24 Aug 2006 (IMPORTANT)
Due to a failure of the main chiller of our building, we have had to switch off some of our machines. Unfortunately, the FUGUE server is down until further notice. Many apologies for the inconvenience and any update will be announced here.
17 May 2006
The server back up but please do refrain from bulk submissions. Once again, thanks for your cooperation.
12 May 2006
Due to a serious hardware problem and increased demands associated with CASP7, we have to block manual submissions to the server temporarily. Please accept our apologies.
19 Apr 2006
The server is back up now.
18 Apr 2006
Due to a hardware problem, the server went down. It is back up now but there is a huge backlog and we decided to stop accepting new submissions for a while. As soon as the situation stabilises, we will open the server again (hopefully by tomorrow). Our apologies for the inconveniences caused.
5 Jul 2005
FUGUE has been installed for command-line use on mole (the main computer for The School of the Biological Sciences). See the documentation.
4 Jul 2005
The latest version of the FUGUE program (2.01) now available for the licensed users.
30 Jun 2005
New homepage is now availble.

Submit your protein sequence




FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.

Here is a summary of how it works.

Read the original paper for more details:

J. Shi, T. L. Blundell, and K. Mizuguchi (2001). FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties. J. Mol. Biol., 310, 243-257.
[PubMed] | [reprint request]

Some practical information can be found in:

R. Nez Miguel, J. Shi and K. Mizuguchi (2001). Protein Fold Recognition and Comparative Modeling using HOMSTRAD, JOY and FUGUE. In Protein Structure Prediction: Bioinformatic Approach. International University Line publishers, La Jolla, 143-169.

Click here for information about the HOMSTRAD database.