19 Jun 1998 Kevin Karplus

No good homologs on target t65

Top scores summing both ways are 
1eaf	-3.680
1eriA	-3.63
1dsl	-3.440
1gamA	-3.300
1gamB	-3.300
1ctn_1	-3.190


Top score is in range
	domains	55 T  627 F	=> 92% false pos
	fssp	10.68T 98.07 F	=> 90% false pos

I'm not even sure it is worth looking at joint models and alignments
with such low scores.

Redid the t98 alignments with new_sam, and got MUCH better results:

			FSSP rep
1ssr	-8.090		?		(theoretical model for synth protein)
1bod	-7.000		5icb		calbindin
1dipA	-6.91		1dipA
1dipB	-6.91		1dipB
2liv	-6.7		2liv
1bfmA	-5.62		1bfmA
1bfmB	-5.370		1bfmA
1pysA	-5.25		1pysA
1boc	-5.070		5icb
1pkp	-4.6		1pkp

None of these proteins is structurally similar to any other.
The higher scores MAY just be a result of differences in SAM score
calibration, though the reversed-sequence scoring should compensate
for that.

Hmm---something strange---2liv is now the best model in the library,
but it wasn't in my notes before, but library models aren't using new_sam.

23 July 1998

The calbindin hit may be worth following up, since there is a weak
match of the end of t64 to calmodulin.  Maybe we should try taking the
last 40 residues of t64 on the beginning of t65?

I think that 1auz and 1buz, which were recently released, may be
possible hits (based on attempts using t66/t66-chim), so I'm going to
redo all the searches.

Best blast hit: 1ois
best double-blast: 1auz, 1buz


Note: the beginning of the SINI sequence matches the end of the SINR
sequence somewhat, so the chimera put together for t66-chim may give
better predictions of the structure than t65 alone.

Top matches for t65.t98_6-varh50 are
	2ci2I=2sniI	-6.53	1ciqA
	1cii		-6.35	1cii
	3ci2		-5.94	1ciqA
	1ssr		-5.58	theoretical
	1ciqA=1cirA	-5.05	1ciqA

Note: the 1ciqA matches get better with t66-chim, the others get worse.

24 July 1998

The best results with the template models are 
	2liv	-5.24
	1eaf	-3.68
	1ctn_1	-3.19

Summing both ways the best results are
	1cii	-7.05	1cii	colicin ia
 2ci2I=2sniI	-6.53	1ciqA	chymotrypsin inhibitor 2
	3ci2	-5.94	1ciqA	chymotrypsin inhibitor 2
	1ssr	-5.58	synthetic
	2liv	-5.24	2liv	leucine-isoleucine-valine binding
	1ciqA	-5.06	1ciqA	chymotrypsin inhibitor 2

The 1cii and 1ciqA scores get worse with t66-chim, but 2liv gets better.

28 July 1998

The hits for t66_7 (with t64, 7X, t65) are so good that I see no point
in further independent work on t65.  I'll use the 1ois alignment from t66.