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Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
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.
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Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Cited by
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
“…tables dependent on structural features such as solvent exposure, secondary structure type, and hydrogen-bonding properties (Shi et al., 2001; Karchin et al., 2003; McGuffin and Jones, 2003; Zhou and Zhou, 2005) or on statistical potentials for residue interactions implied by the alignment…”
BackgroundMethodPhylogenomic analysis of the GIY-YIG nuclease superfamily
Dunin-Horkawicz, S., Feder, M., & Bujnicki, J. M. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-98 · Cited by 133
Hawtin, S. R., Wesley, V. J., Simms, J., Argent, C. C. H., Latif, K., & Wheatley, M. (2005) · Molecular Endocrinology · doi:10.1210/me.2005-0148 · Cited by 24
Metadata
- Authors
- Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., & Hughey, R.
- Venue
- Proteins: Structure, Function, and Genetics
- Publisher
- Wiley
- Published
- 2003
- Volume
- 53
- Issue
- S6
- Pages
- 491-496
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2106066024
- Cited by
- 294
- References
- 1
- FWCI
- 8.15
- Type
- journal article
- Language
- en
- Open access
- closed
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- Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., & Hughey, R. (2003). Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins: Structure, Function, and Genetics. https://doi.org/10.1002/prot.10540
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