title: SAM-T08, HMM-based protein structure prediction.
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.
authors.affiliation: Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA. karplus@soe.ucsc.edu
authors.forename: Kevin
authors.initials: K
authors.lastname: Karplus
mesh_terms: D030562:Databases, Protein; D008390:Markov Chains; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins