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.
Computer Engineering Department, University of California, Santa Cruz 95064, USA. karplus@soe.ucsc.edu
Kevin
K
Karplus
Rachel
R
Karchin
Jenny
J
Draper
Jonathan
J
Casper
Yael
Y
Mandel-Gutfreund
Mark
M
Diekhans
Richard
R
Hughey
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins