PFRMAT TS 
TARGET T0061 
REMARK ======================================================================= 
AUTHOR 2738-1421-4442 
REMARK This prediction was prepared by Anna Panchenko, 
REMARK Aron Marchler-Bauer, and Steve Bryant, NCBI.  
REMARK ======================================================================= 
METHOD Predictions were made with the potential and alignment model used in 
METHOD CASP1 and CASP2 predictions, as described by Madej et al. in Proteins 
METHOD 23:356-369, 1995. Convergence control has been added to the Gibbs- 
METHOD Sampling alignment model. In addition to contact-based threading 
METHOD potentials, PSSMs summarizing sequence conservation in the family 
METHOD represented by the template structure are used to score threading 
METHOD alignments. Threading "cores" summarizing the conserved substructure 
METHOD in the templates used for models below have been based on structure 
METHOD superpositions generated by VAST (Gibrat et al., Curr Opin Struct 
METHOD Biol 1996 Jun;6(3):377-385 ). 
METHOD The alignments have been calculated with the Gibbs Sampling threading 
METHOD engine. No single template has been identified in threading database 
METHOD searches with unambiguous scores/p-values. We therefore submit "NONE" 
METHOD as model no. 1, indicating that the automated search methods have not 
METHOD indicated a clearly favored template. Additional models represent  
METHOD top-scoring hits from threading database searches, models 2 and 3 
METHOD have been calculated using PSSM-based scoring, and models 4 and 5 with 
METHOD the contact-based threader. 
REMARK ======================================================================= 
MODEL  1 
PARENT NONE 
TER 
END 
