Nucleic Acids Research Advance Access originally published online on May 29, 2009
Nucleic Acids Research 2009 37(Web Server issue):W492-W497; doi:10.1093/nar/gkp403
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W492-W497
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
SAM-T08, HMM-based protein structure prediction
Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
*To whom correspondence should be addressed. Tel: +1831 459 4250; Email: karplus{at}soe.ucsc.edu
Received January 30, 2009. Revised April 20, 2009. Accepted May 2, 2009.
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