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 10 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. 
        O_NOTOR2 an alphabet for predicting characteristics of hydrogen
		bonds from the carbonyl oxygen
	N_NOTOR2 an alphabet for predicting characteristics of hydrogen
		bonds from the amide nitrogen
    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
    8000 (t06), 10000 (t04), or 15000 (t2k) 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).

    Generate fragments (short 9-residue alignments for each position)
    using SAM's "fragfinder" program and the 3-track HMM which tested
    best for alignment.

    Residue-residue contact predictions are made using mutual
    information, pairwise contact potentials, joint entropy, and other
    signals combined by a neural net.  The contact prediction method
    is expected to evolve over the summer, as new features are
    selected and new networks trained.
    
    Then the "undertaker" program (named because it optimizes burial)
    is used to try to combine the alignments and the fragments into a
    consistent 3D model.  No single alignment or parent template was
    used as a frozen core, though in many cases one had much more
    influence than the others.  The alignment scores were not passed
    to undertaker, but were used only to pick the set of alignments
    and fragments that undertaker would see.  Helix and strand
    constraints generated from the secondary-structure predictions are
    passed to undertaker to use in the cost function, as are the
    residue-residue contact prediction.

    One important change in this server over previous methods is that
    sheet constraints are extracted from the top few alignments and
    passed to undertaker. 

After the automatic prediction is done, we examine it by hand and try
to fix any flaws that we see.  This generally involves rerunning
undertaker with new cost functions, increasing the weights for
features we want to see and decreasing the weights where we think the
optimization has gone overboard.  Sometimes we will add new templates
or remove ones that we think are misleading the optimization process.


Model 1 is try16-opt2. It is almost identical to try3, which was an
automatic run that ended up making only relatively minor adjustments
to 1jg5A. 1jg5 is a pentamer, but in this case undertaker stayed very
close to the template so pentamer optimization was deemed unnecessary
to improve the monomer structure.

Model 2 is try17-opt2, a slight re-optimization of try6. Try6 was an
automatic run but with two templates in the d.205.1 SCOP superfamily
removed (1jg5A is in d.205.1). It seems to be mostly fragment packing.

Model 3 is try19-opt2.gromacs0.repack-nonPC, based in turn on
try13. Here we have tried to make the predicted third strand
anti-parallel to the first part of the first strand.  The
undertaker-optimized model try19-opt2 was then reoptimized with
gromacs and the sidechains were repacked by rosetta.  This is
rosetta's favorite of the backbones for which it repacked sidechains.

Model 4 is try15-opt2, based on a version of try10 edited in
ProteinShop to move one of the helices to a more sensible
position. The second helix is supposed to be a loop, and the final
helix was an anti-parallel strand in try10, but undertaker likes
helices. Try10 was again an attempt to make the third strand
anti-parallel to first part of the first strand.

Model 5 is try9-opt2. This was an attempt to make the third strand
parallel to the first part of the first strand.