This server was tested as SAM_T06_server in the CASP7 and CASP8 experiments. Preliminary results indicate that it is an OK primary server, but has been clearly surpassed by SAM_T08 at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html
Please switch to the SAM-T08 server.
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 alpahbets, 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 31 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 firstname.lastname@example.org
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 February 09, 2009.