SAM_T08 Results for NP_510002_1

Please cite the following papers:

• Kevin Karplus. SAM-T08: HMM-based Protein Structure Prediction. Nucleic Acids Research 2009, Web Server Issue. Nucleic Acids Research Advance Access published online on May 29, 2009. doi:10.1093/nar/gkp403 [This paper covers the SAM-T08 web server, but not the underlying methods.]
• Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and Kevin Karplus. Predict-2nd: a tool for generalized protein local structure prediction. Bioinformatics 2008 24: 2453-2459
  Free Reprint:http://bioinformatics.oxfordjournals.org/cgi/reprint/btn438?
  doi:10.1093/bioinformatics/btn438 [This paper is relevant for the secondary structure, burial, or other local structure predictions.]

• George Shackelford and Kevin Karplus. Contact Prediction using Mutual Information and Neural Nets. Proteins: Structure, Function, and Bioinformatics, 69(S8):159-164, 2007. (CASP7 special issue).
  doi:10.1002/prot.21791 Preprint [This paper is relevant for the contact predictions.]

• 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 [This paper is relevant for the overall method and tertiary structure predictions.]

• 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 [This paper is relevant for the burial predictions.]

• 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 [This paper is relevant for the overall method and tertiary structure predictions.]
• 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 [This paper is relevant for the secondary-structure predictions.]
• 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 [This paper is relevant for the overall method and tertiary structure predictions.]