The SAM-T06 hand predictions use methods similar to SAM_T04 in CASP6 and
the SAM-T02 method in CASP5.

We start with a fully automated method (implemented as the SAM_T06 server):
   
    Use the SAM-T2K and SAM-T04 methods for finding homologs of the
    target and aligning them.  The hand method also uses the
    experimental new SAM-T06 alignment method, which we hope is both
    more sensitive and lass prone to contamination by unrelated sequences.

    Make local structure predictions using neural nets and the
    multiple alignments.  
      
    We currently use 8 local-structure alphabets: 
	DSSP
	STRIDE
	STR2	an extended version of DSSP that splits the beta strands
		into multiple classes (parallel/antiparallel/mixed,
					edge/center)
	ALPHA	an discretization of the alpha torsion angle:
		CA(i-i), CA(i), CA(i+1), CA(i+2)
	BYS	a discretization of Ramachandran plots, due to Bystroff
	CB_burial_14_7	a 7-state discretization of the number of C_beta
		atoms in a 14 Angstrom radius sphere around the C_beta.
	near-backbone-11 an 11-state discretization of the number of
	      residues (represented by near-backbone points) in a 
	      9.65 Angstrom radius sphere around the sidechain proxy
	      spot for the residue.
	DSSP_EHL2	CASP's collapse of the DSSP alphabet
			DSSP_EHL2 is not predicted directly by a
			neural net, but is computed as a weighted
			average of the other backbone alphabet predictions. 
    We hope to add more networks for other alphabets over the summer.
    
    We make 2-track HMMs with each alphabet (1.0 amino acid + 0.3
    local structure) and use them to score a template library of about
    10000 (t04) or 15000 (t2k) templates (the t06 library is still
    being built, and is expected to have around 8000 templates).
    The template libraries are expanded weekly, but old template HMMs
    are not rebuilt.
    
    We also used a single-track HMM to score not just the template
    library, but a non-redundant copy of the entire PDB.

    One-track HMMs built from the template library multiple alignments
    were used to score the target sequence.

    All the logs of e-values were combined in a weighted average (with
    rather arbitrary weights, since we still have not taken the time
    to optimize them), and the best templates ranked.  
    
    Alignments of the target to the top templates were made using
    several different alignment methods (mainly using the SAM hmmscore
    program, but a few alignments were made with Bob Edgar's MUSCLE
    profile-profile aligner).

This prediction has no optimization done, but just SCWRL-based
sidechain replacement on alignment 
T0288-1g9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5