Sun Dec 19 16:15:38 PST 2010 Kevin Karplus

In ../training-data
ran
make dunbrack-30pc-1763-1.pb-aa dunbrack-30pc-1763-2.pb-aa dunbrack-30pc-1763-3.pb-aa
to create the pb->aa training and testing files.

Ran "make dirs" to create directories and
created networks/Gpb-5-20-5-20-5-aa-empty.net
based on similar network in ../str2uc-near-backbone-11-20_rev/networks

Mon Dec 20 17:03:44 PST 2010 Kevin Karplus

bit gain (from quality-reports/)			
epochs	arch			tr12avg	tr12best	tr23avg	tr23best	tr31avg	tr31best
50	pb-5-20-5-20-5		0.19049	0.2148		0.18774	0.2110		0.18409	0.2095

str2uc-near-backbone-11-20:
50	5-20-5-20-5		0.16974	0.2155		0.16786	0.2007		0.17164	0.2064
150	5-20-5-20-5		0.28647	0.2937		0.2799	0.2860		0.28202	0.2891
250	5-20-5-20-5		0.31713	0.3178		0.31117	0.3114		0.3123	0.3175
test	5-20-5-20-5			0.3072			0.3075			0.3123

50	bys-3-11-5-11-7-11-9	0.21049	0.2630		0.20551	0.2719		0.20105	0.2640
150	bys-3-11-5-11-7-11-9	0.33736	0.3509		0.33729	0.3522		0.33606	0.3437
250	bys-3-11-5-11-7-11-9	0.37357	0.3759		0.3717	0.3762		0.3639	0.3605
test	bys-3-11-5-11-7-11-9		0.3647			0.3663			0.3665

50	nb11-3-5-22-7-11-9	0.1285	0.2118		0.13003	0.2147		0.12271	0.2136
150	nb11-3-5-22-7-11-9	0.24283	0.2478		0.24245	0.2512		0.24144	0.2478
250	nb11-3-5-22-7-11-9	0.25907	0.2605		0.26177	0.2622		0.25847	0.2611
test	nb11-3-5-22-7-11-9		0.2555			0.2569			0.2539

50	str2-3-13-5-13-7-13-9	0.09692	0.1536		0.09414	0.1485		0.09189	0.1432
150	str2-3-13-5-13-7-13-9	0.20104	0.2092		0.2003	0.2079		0.2007	0.2070
250	str2-3-13-5-13-7-13-9	0.22793	0.2291		0.22697	0.2307		0.2277	0.2299
test	str2-3-13-5-13-7-13-9		0.2209			0.2244			0.2250

50	dssp-3-8-5-8-5-8-7	0.14064	0.1677		0.1399	0.1597		0.13785	0.1567
150	dssp-3-8-5-8-5-8-7	0.19263	0.1965		0.19206	0.1966		0.19065	0.1961
250	dssp-3-8-5-8-5-8-7	0.20693	0.2084		0.207	0.2093		0.20757	0.2098
test	dssp-3-8-5-8-5-8-7		0.1993			0.2048			0.2089

Sun Dec 26 09:27:41 PST 2010 Kevin Karplus

bit gain (from quality-reports/)			
epochs	arch			tr12avg	tr12best	tr23avg	tr23best	tr31avg	tr31best
50	pb-5-20-5-20-5		0.19049	0.2148		0.18774	0.2110		0.18409	0.2095
150	pb-5-20-5-20-5		0.24855	0.2547		0.24713	0.2523		0.24482	0.2502

Sun Dec 26 15:25:52 PST 2010 Kevin Karplus

bit gain (from quality-reports/)			
epochs	arch			tr12avg	tr12best	tr23avg	tr23best	tr31avg	tr31best
50	pb-5-20-5-20-5		0.19049	0.2148		0.18774	0.2110		0.18409	0.2095
150	pb-5-20-5-20-5		0.24855	0.2547		0.24713	0.2523		0.24482	0.2502
250	pb-5-20-5-20-5		0.2684	0.2809		0.26637	0.2684		0.26377	0.2661
test	pb-5-20-5-20-5			0.2599			0.2622			0.2660

Sequence recovery
test	pb-5-20-5-20-5			16.75%			16.94%			16.91%


Mon Dec 27 15:26:20 PST 2010 Kevin Karplus

I've made some minor modifications to predict-2nd to test RDB output
of predictions.