HMM-based Protein Structure Prediction, SAM-T08

As of noon(Pacific time) 2 March 2009, the web service should be back up. If you have troubles with it, please inform and we will try to get the techstaff to fix the problem promptly.

This server was tested as SAM_T08_server in the CASP8 experiment. Preliminary results indicate that it is a good primary server, but that metaservers combining results from several primary servers are likely to produce somewhat better results.

This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed. Look carefully at the E-values for the best hits, as full 3D models are constructed even when the E-values are high (and the resulting models are not then not trustworthy).

As of 26 Jan 2009, running on "bmecluster", rather than the "moai" cluster. This is the same hardware, but a different operating system (now using the "Rocks" version of Linux), which necessitated many little changes to the scripts and makefiles. Please report strange behavior to

Email Address (required):  
Subject line:  
Email the secondary structure predictions (CASP SS format).  Subject line:
Email the residue-residue contact predictions (CASP RR format).  Subject line:
Email the top 5 models (CASP TS format).  Subject line:

  • Either cut and paste your FASTA-formatted sequence directly in the box below:

  • ...or else upload it from a file on your local system, using the button below:


You can find an explanation of common errors on our SAM-T08 frequently-asked questions page (FAQ). If you do not find a solution to your problem there, please inform us at

If you checked any of the "email me" boxes in Step 1, you will receive an email when your query is complete. You can also just wait for the resulting page to load (this could take a while, depending on how many other requests we are currently processing).

This server has evolved over the years under the direction of Kevin Karplus. Major contributors to the web design include Alex Williams, Rachel Karchin, Spencer Tu, and Christian Barrett.

This document was last modified on September 18, 2009.