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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W492-7. doi: 10.1093/nar/gkp403. Epub 2009 May 29.

SAM-T08, HMM-based protein structure prediction.

Author information

1
Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA. karplus@soe.ucsc.edu

Abstract

The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue-residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html.

PMID:
19483096
PMCID:
PMC2703928
DOI:
10.1093/nar/gkp403
[Indexed for MEDLINE]
Free PMC Article

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