Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139.
Karplus
Kevin
K
Computer Engineering Department, University of California, Santa Cruz 95064, USA. karplus@soe.ucsc.edu
Karchin
Rachel
R
Draper
Jenny
J
Casper
Jonathan
J
Mandel-Gutfreund
Yael
Y
Diekhans
Mark
M
Hughey
Richard
R
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins