Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper,
Bret Barnes, Marcia Soriano, and Richard Hughey.
SAM-T04: what's new in protein-structure prediction for CASP6.
Proteins: Structure, Function, and Bioinformatics, 2005.
61(S7):135-142.
doi:10.1002/prot.20730
Rachel Karchin, Melissa Cline, and Kevin Karplus.
Evaluation of local structure alphabets based on residue burial.
Proteins: Structure, Function, and Genetics, 55(3):508--518, 5 March 2004.
doi:10.1002/prot.20008
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus.
Hidden Markov models that use predicted local structure for fold
recognition: alphabets of backbone geometry.
Proteins: Structure, Function, and Genetics, 51(4):504--514,
June 2003.
doi:10.1002/prot.10369
Karplus, K. and Karchin, R. and Draper, J. and Casper, J. and Mandel-Gutfreund, Y. and Diekhans, M. and Hughey, R.
``Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction''
Proteins: Structure Function and Genetics53(S6):491-496,15 Oct 2003
doi:10.1002/prot.10540
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus.
``Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.''
Proteins: Structure, Function, and Genetics, 51(4):504--514, June 2003.
doi:10.1002/prot.10369
Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R.
``What is the value added by human intervention in protein structure prediction?''
Proteins: Structure Function and Genetics 45(S5):86-91,2001
doi:10.1002/prot.10021
When SAM_T06 finishes loading, you should see links to
Inputs and Multiple Alignments
Secondary Structure Prediction
Target model scores with annotation
Template model scores with annotation
Top Hits—best scoring templates from all models
Alignments for Top Hits
Sidechain-replacement models using backbones from templates
Residue-residue contact predictions
Complete model for target sequence
The page uses a "meta" tag to automatically refresh every
4 minutes.
You may also view the list of files
created so far.
This link gives access to the full directory of
file produced, including query progress logs, and this html file
(summary.html).
When the process is finished, you may want to download the
entire directory to your computer, using a tool such as "wget".