Wed Aug 11 10:40:13 PDT 2004
T0274

DUE 31 Aug 2004


Wed Aug 11 12:29:33 PDT 2004 Kevin Karplus

comparative model with 1rz1A and other b.45.1.2 templates.

It is not clear whether the t2k or t04 alignment is better for this
target---they have fairly similar conservation patterns, but the t04
alignment is deeper.  It may not matter, as we have full-length
alignment with only 3 small gaps for the top templates.

This looks like a pretty easy target---I should be able to get it
submitted by tomorrow.


Wed Aug 11 16:13:47 PDT 2004 Kevin Karplus

try1-opt2 looks good.

I'll do a polishing run with an unconstrained costfcn.


Fri Aug 13 11:59:06 PDT 2004 Kevin Karplus

try2-opt2 also looks good.

I picked up the robetta models, and scored everything with unconstrained.costfcn
try2-opt2 scores best.

Rosetta likes try2-opt2.repack-nonPC better than try1, but still
thinks there are clashes (of course, undertaker thinks that the
robetta models have clashes, so this may just be differences of
opinion about how bad the clashes are).

I'll submit
	try2-opt2	best undertaker score
	try2-opt2.repack-nonPC	best rosetta energy
	try1-opt2	full auto
	T0274-1rz1A-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5	
	T0274-1i0sA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5

Thu Nov 18 23:54:41 PST 2004	Martina Koeva

Based on the smooth gdt scores:

best sam-t04	66.3979 (also our align2)
best submit	65.8941 (model4)
model1		60.2917
auto		60.8360
align		65.9052
robetta best	68.2231 (robetta model2)
robetta1	66.6229