Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
Citations Over TimeTop 10% of 2003 papers
Abstract
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.
Related Papers
- → Intrinsic Disorder in the Protein Data Bank(2007)171 cited
- → Changing in fold geometry from faulted detachment fold to fault-bend fold, a case study: The Zeloi Anticline in the Dezful Embayment, southwest of Iran(2018)21 cited
- PDB-REPRDB: a database of representative protein chains in PDB (Protein Data Bank).(1997)
- → A FRAGMENT ON DIFFERENCE(2004)2 cited
- → Interactions between surface processes and fold growth in fold-and-thrust belts: application to the Zagros Fold Belt(2015)1 cited