PFRMAT AL 
TARGET T0077 
REMARK ======================================================================= 
AUTHOR 2738-1421-4442 
REMARK This prediction was prepared by Anna Panchenko, Aron Marchler-Bauer, 
REMARK 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 may 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. Models based on 1WHI have been identified with a PSSM-based 
METHOD scoring scheme with P-values at the borderline of significance.  
METHOD Models based on 1RIS gave significant scores with the contact-based 
METHOD threader. Model 1: PSSM, weight 1.0.  
METHOD           Model 2: contact-based 
METHOD           Model 3: contact-based 
METHOD           Model 4: PSSM, weight 0.5 
METHOD           Model 5: We have added "NONE" to express limited confidence 
METHOD in the prediction, since we have seen interesting hits to two very 
METHOD different  
REMARK ======================================================================= 
MODEL  5 
PARENT NONE 
TER 
END 
