some analysis about barrals with sandwich's HMM

g1rin.1: 13B.fa 121.5 5.1e-35 1
looks more like a sandwich to me then barral.

g1ghw.1: 1F.fa 121.2 6.2e-35 1
looks like barral, but has interlock.

d1eu3a1: 20B.fa -46.2 1.8e+02 1
a barral looks like sandwich.
but I agree it's a barral, since I didn't saw a sandwich in this angle.

d3vub__: 20B.fa -49.6 1.8e+02 1
two barral share one wall, like "8" shape

d1jb3a_: 20B.fa -42.4 1.8e+02 1
barral
1 2 3 5 4

4 1 2'
5 3 2

d3chbd_: 20B.fa -44.5 1.8e+02 1
motif 20B only has one structure which doesn't looks like a regular sandwich.
d3chbd_ looks like a distorted barral, which looks like a distorted sandwich also.

d1jzua_: 20B.fa -36.6 1.8e+02 1
jelly roll, probably because of the strands length, it almost form a sandwich like structure.

3V
a motif doesn't have interlock.

d1qb5d_: 3V.fa -44.2 1.8e+02 1
there's one sheet which looks like sandwich's sheet.

d1g7sa1: 3V.fa -45.3 1.8e+02 1
probably because the additional sheets in barral

some of these structures have alpha helix, so our HMM probably can't recognize it perfectly.

d1ewna_: 2G.fa -22.0 1.8e+02 1
have lots of alpha helix

d1ja1a1: 2G.fa -10.2 1.8e+02 1
have lots of alpha helix in this domain

d1f20a1: 2G.fa -13.9 1.8e+02 1
have lots of alpha helix in this domain

d1i4ua_: 2G.fa -29.0 1.8e+02 1

the training set we train HMM has already been modified before grouping, but the sequences we train it doesn't.

predict barral structures using sandwich motif HMMs

d1ep3b1: 2G.fa -40.7 1.8e+02 1
d1et9a1: 2G.fa -35.3 1.8e+02 1
d1eu3a1: 20B.fa -46.2 1.8e+02 1
d1bw3__: 2G.fa -39.8 1.8e+02 1
d1ne8a_: 2G.fa -33.6 1.8e+02 1
d1nnxa_: 2G.fa -41.6 1.8e+02 1
d1iiua_: 2G.fa -34.5 1.8e+02 1
d1kt7a_: 2G.fa -36.1 1.8e+02 1
d1rbp__: 2G.fa -36.6 1.8e+02 1
d1l6ma_: 2G.fa -30.8 1.8e+02 1
d1ewna_: 2G.fa -22.0 1.8e+02 1
d1nrga_: 2G.fa -40.3 1.8e+02 1
d1ow1a_: 2G.fa -39.1 1.8e+02 1
d1uapa_: 2G.fa -42.5 1.8e+02 1
d1ueab_: 2G.fa -33.1 1.8e+02 1
d3vub__: 20B.fa -49.6 1.8e+02 1
d1m1fa_: 2G.fa -46.8 1.8e+02 1
d1ub4a_: 2G.fa -38.5 1.8e+02 1
d1qoia_: 2G.fa -37.9 1.8e+02 1
d1a33__: 2G.fa -38.9 1.8e+02 1
d1qnga_: 2G.fa -42.3 1.8e+02 1
d1ista_: 2G.fa -29.6 1.8e+02 1
d1ihga2: 2G.fa -37.3 1.8e+02 1
d2cpl__: 2G.fa -37.1 1.8e+02 1
d1dywa_: 2G.fa -33.8 1.8e+02 1
d1h0pa_: 2G.fa -35.2 1.8e+02 1
d2rmca_: 2G.fa -31.4 1.8e+02 1
d1cyna_: 2G.fa -37.8 1.8e+02 1
d1liua1: 2G.fa -46.1 1.8e+02 1
d1sr3a_: 2G.fa -37.9 1.8e+02 1
d1jb3a_: 20B.fa -42.4 1.8e+02 1
d1xe1a_: 24A.fa -42.4 1.8e+02 1
g1rin.1: 13B.fa 121.5 5.1e-35 1
d1k0ha_: 2G.fa -51.4 1.8e+02 1
g1ghw.1: 1F.fa 121.2 6.2e-35 1
d3chbd_: 20B.fa -44.5 1.8e+02 1
d1ssxa_: 2G.fa -38.9 1.8e+02 1
d1rz0a_: 2G.fa -29.8 1.8e+02 1
d1i8da1: 2G.fa -45.6 1.8e+02 1
d1ogia1: 2G.fa -33.5 1.8e+02 1
d1jb9a1: 2G.fa -37.7 1.8e+02 1
d1gawa1: 2G.fa -37.7 1.8e+02 1
d1fnc_1: 2G.fa -38.6 1.8e+02 1
d1qfza1: 2G.fa -31.1 1.8e+02 1
d1sm4a1: 2G.fa -32.0 1.8e+02 1
d1qb5d_: 3V.fa -44.2 1.8e+02 1
d1ja1a1: 2G.fa -10.2 1.8e+02 1
d1f20a1: 2G.fa -13.9 1.8e+02 1
d1mabb2: 2G.fa -47.3 1.8e+02 1
d1w0jd2: 2G.fa -45.2 1.8e+02 1
d1kmha2: 2G.fa -48.2 1.8e+02 1
d1skyb2: 2G.fa -51.1 1.8e+02 1
d1w0ja2: 2G.fa -52.3 1.8e+02 1
d1skye2: 2G.fa -38.8 1.8e+02 1
d1kmhb2: 2G.fa -47.0 1.8e+02 1
d1o65a_: 2G.fa -38.1 1.8e+02 1
d1i0ra_: 2G.fa -43.2 1.8e+02 1
d1eova1: 2G.fa -34.8 1.8e+02 1
d1n0ua1: 2G.fa -44.0 1.8e+02 1
d1ci0a_: 3V.fa -36.7 1.8e+02 1
d1f60a2: 2G.fa -45.8 1.8e+02 1
d1kzla1: 2G.fa -34.1 1.8e+02 1
d1n08a_: 2G.fa -47.2 1.8e+02 1
d1nb0a_: 2G.fa -38.3 1.8e+02 1
d1epaa_: 2G.fa -36.7 1.8e+02 1
d1jzua_: 20B.fa -36.6 1.8e+02 1
d1a1x__: 20B.fa -51.2 1.8e+02 1
d1jnpa_: 2G.fa -44.9 1.8e+02 1
d1i4ua_: 2G.fa -29.0 1.8e+02 1
d1kxoa_: 2G.fa -33.8 1.8e+02 1
d1nf3c_: 2G.fa -39.8 1.8e+02 1
d1qz8a_: 2G.fa -44.5 1.8e+02 1
d1r2ma_: 2G.fa -40.1 1.8e+02 1
d1g7sa1: 3V.fa -45.3 1.8e+02 1
d1qfja1: 2G.fa -47.3 1.8e+02 1
d1kjwa1: 2G.fa -44.8 1.8e+02 1
d1jj2b_: 2G.fa -22.2 1.8e+02 1
d1qvca_: 2G.fa -35.2 1.8e+02 1
d1qx4a1: 2G.fa -45.3 1.8e+02 1
d2cnd_1: 2G.fa -37.1 1.8e+02 1
d1fx7a3: 2G.fa -46.3 1.8e+02 1
d1g3wa3: 2G.fa -43.7 1.8e+02 1
d1vl7a_: 2G.fa -42.2 1.8e+02 1
d1prtf_: 2G.fa -46.1 1.8e+02 1
d1krha1: 2G.fa -44.7 1.8e+02 1
d1a8p_1: 2G.fa -35.0 1.8e+02 1
d2qila1: 2G.fa -44.2 1.8e+02 1
d1pc0a_: 2G.fa -44.6 1.8e+02 1
d1skqa1: 2G.fa -47.9 1.8e+02 1
d1skqa2: 2G.fa -34.5 1.8e+02 1
d1d1na_: 2G.fa -47.7 1.8e+02 1
d1qnua_: 2G.fa -44.2 1.8e+02 1
d1cqxa2: 2G.fa -36.1 1.8e+02 1
d1udza_: 2G.fa -35.7 1.8e+02 1
d1c0aa1: 2G.fa -39.1 1.8e+02 1
d1n9wa1: 2G.fa -43.7 1.8e+02 1
d1l0wa1: 2G.fa -46.1 1.8e+02 1
d1kk1a1: 2G.fa -34.9 1.8e+02 1
d1kk1a2: 2G.fa -37.1 1.8e+02 1
d1d2ea2: 2G.fa -45.4 1.8e+02 1
d1efca2: 2G.fa -43.2 1.8e+02 1
d1eft_2: 2G.fa -37.1 1.8e+02 1
d1exma2: 2G.fa -39.7 1.8e+02 1
d1bbua1: 2G.fa -37.9 1.8e+02 1
d1e1oa1: 2G.fa -33.3 1.8e+02 1
d1fdr_1: 2G.fa -33.6 1.8e+02 1
d1fmta1: 2G.fa -41.2 1.8e+02 1
d1gvha2: 2G.fa -36.3 1.8e+02 1
d1v9ta_: 2G.fa -37.5 1.8e+02 1
d1dar_1: 2G.fa -46.7 1.8e+02 1
d1ixra2: 2G.fa -48.4 1.8e+02 1
d1usca_: 2G.fa -27.0 1.8e+02 1
d1dnla_: 2G.fa -40.3 1.8e+02 1
d1d2ea1: 2G.fa -40.9 1.8e+02 1
d1efca1: 2G.fa -37.6 1.8e+02 1
d1eft_1: 2G.fa -39.7 1.8e+02 1
d1exma1: 2G.fa -39.7 1.8e+02 1
d1cuk_3: 2G.fa -46.8 1.8e+02 1
d1ddga1: 2G.fa -29.3 1.8e+02 1
/119

next step: check why barrals similar to sandwich's motif 2G.
simple findings:
2G*107
20B*5
24A*1
13B!
1F!
3V*3

other paper predict EP/NEP

This paper they try to predict edge and non-edge
ß Edge strands in protein structure prediction and aggregation
Their prediction accuracy is 78%
The attributes they use, are (1) bulge score, (2) charge score, (3) hydrophobicity, (4) hydrophobic moment, (5) pattern of polarity, and (6) strand length.