Bioinformatics, Vol 14, 846-856, Copyright © 1998 by Oxford University Press
K Karplus, C Barrett and R Hughey
MOTIVATION: A new hidden Markov model method (SAM-T98) for finding remote
homologs of protein sequences is described and evaluated. The method begins
with a single target sequence and iteratively builds a hidden Markov model
(HMM) from the sequence and homologs found using the HMM for database
search. SAM-T98 is also used to construct model libraries automatically
from sequences in structural databases. METHODS: We evaluate the SAM-T98
method with four datasets. Three of the test sets are fold-recognition
tests, where the correct answers are determined by structural similarity.
The fourth uses a curated database. The method is compared against
WU-BLASTP and against DOUBLE- BLAST, a two-step method similar to ISS, but
using BLAST instead of FASTA. RESULTS: SAM-T98 had the fewest errors in all
tests-dramatically so for the fold-recognition tests. At the minimum-error
point on the SCOP (Structural Classification of Proteins)-domains test,
SAM-T98 got 880 true positives and 68 false positives, DOUBLE-BLAST got 533
true positives with 71 false positives, and WU-BLASTP got 353 true
positives with 24 false positives. The method is optimized to recognize
superfamilies, and would require parameter adjustment to be used to find
family or fold relationships. One key to the performance of the HMM method
is a new score-normalization technique that compares the score to the score
with a reversed model rather than to a uniform null model. AVAILABILITY: A
World Wide Web server, as well as information on obtaining the Sequence
Alignment and Modeling (SAM) software suite, can be found at
http://www.cse.ucsc.edu/research/compbi o/ CONTACT: karplus@cse.ucsc.edu;
http://www.cse.ucsc.edu/~karplus
ARTICLES
Hidden Markov models for detecting remote protein homologies
Department of Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.
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I. Rigoutsos, P. Riek, R. M. Graham, and J. Novotny Structural details (kinks and non-{alpha} conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors Nucleic Acids Res., August 1, 2003; 31(15): 4625 - 4631. [Abstract] [Full Text] [PDF]
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B. John and A. Sali Comparative protein structure modeling by iterative alignment, model building and model assessment Nucleic Acids Res., July 15, 2003; 31(14): 3982 - 3992. [Abstract] [Full Text] [PDF]
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V. A. Eyrich and B. Rost META-PP: single interface to crucial prediction servers Nucleic Acids Res., July 1, 2003; 31(13): 3308 - 3310. [Abstract] [Full Text] [PDF]
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I. Y. Y. Koh, V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M. S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, et al. EVA: evaluation of protein structure prediction servers Nucleic Acids Res., July 1, 2003; 31(13): 3311 - 3315. [Abstract] [Full Text] [PDF]
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M. Albrecht, S. C.E. Tosatto, T. Lengauer, and G. Valle Simple consensus procedures are effective and sufficient in secondary structure prediction Protein Eng. Des. Sel., July 1, 2003; 16(7): 459 - 462. [Abstract] [Full Text] [PDF]
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 T. S. Furey and D. Haussler Integration of the cytogenetic map with the draft human genome sequence Hum. Mol. Genet., May 1, 2003; 12(9): 1037 - 1044. [Abstract] [Full Text] [PDF]
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B. Cooper, J. D. Clarke, P. Budworth, J. Kreps, D. Hutchison, S. Park, S. Guimil, M. Dunn, P. Luginbuhl, C. Ellero, et al. A network of rice genes associated with stress response and seed development PNAS, April 15, 2003; 100(8): 4945 - 4950. [Abstract] [Full Text] [PDF]
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D. Fischer and L. Rychlewski The 2002 Olympic Games of Protein Structure Prediction Protein Eng. Des. Sel., March 1, 2003; 16(3): 157 - 160. [Abstract] [Full Text] [PDF]
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A. Cronin, S. Mowbray, H. Durk, S. Homburg, I. Fleming, B. Fisslthaler, F. Oesch, and M. Arand The N-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase PNAS, February 18, 2003; 100(4): 1552 - 1557. [Abstract] [Full Text] [PDF]
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M. Madan Babu and S. A. Teichmann Evolution of transcription factors and the gene regulatory network in Escherichia coli Nucleic Acids Res., February 15, 2003; 31(4): 1234 - 1244. [Abstract] [Full Text] [PDF]
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B. M. Swalla, R. I. Gumport, and J. F. Gardner Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain Nucleic Acids Res., February 1, 2003; 31(3): 805 - 818. [Abstract] [Full Text] [PDF]
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F. M. G. Pearl, C. F. Bennett, J. E. Bray, A. P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, and C. A. Orengo The CATH database: an extended protein family resource for structural and functional genomics Nucleic Acids Res., January 1, 2003; 31(1): 452 - 455. [Abstract] [Full Text] [PDF]
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