Fri Aug 13 11:22:30 PDT 2004
T0276

Fri Aug 13 21:07:58 PDT 2004 Kevin Karplus

Comparative model with 1souA as sole template, though some other
templates come out (though much weaker) in t2k and t04 predictions:
1g2iA 1f8yA (both from c.23 fold, though different superfamilies).

Try1-opt2 looks pretty good.  Just a little foamy.

I'll do an optimization with an unconstrained cost function and call
it done.

(Maybe I'd better check the conserved residues and their neighbors to
see if there is an active or metal-binding site to clean up.)


Sat Aug 14 14:36:27 PDT 2004 Kevin Karplus

try2-opt2 scores better than try1 and looks pretty good.  There is bit
of foaminess around the charged residues, and I'm not sure if the
conserved polars (the active site?) cluster as tightly as they ought
to.   I don't think I'll make much difference here, though, so I'll
just submit this as is:
	try2-opt2	best undertaker
	try2-opt2.repack-nonPC	best Rosetta	(still sees bad clashes)
	try1-opt2	full auto
	T0276-1souA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5
	T0276-1g2iA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5
	
Thu Nov 18 23:55:19 PST 2004	Martina Koeva

Based on the smooth gdt scores:

best sam-t04	64.9133 (try2-opt1)
best submit	64.5671 (model2)
model1		64.5646
auto		63.7876
align		62.6270
robetta best	62.6321 (robetta model3)
robetta1	62.0465