Optimal reduced alphabets and RMSD from original
CMFILVWYAGTSNQDEHRKP 483.3916
CMFILVWY AGTSNQDEHRKP 75.8647
CMVWY FIL AGTSNQDEHRKP 41.3897
CMVWY FIL AGTHP SNQDERK 24.8116
CMVWY FIL AH GTSNQRP DEK 18.8571
CY MVW FIL AH GTSQRP NDE K 10.9412
CY MVW FIL AH GTP SNQR DE K 8.8100
It is worth noting that the optimal five bead is very nearly that of Cieplak's.
Using the RMSD from the full matrix calculation:
CMVWY FIL AH GTSQRP NDEK 0.2897
[[ 4.969 5.973 3.739 3.159 2.654]
[ 5.973 7.054 4.625 3.991 3.412]
[ 3.739 4.625 2.647 2.122 1.783]
[ 3.159 3.991 2.122 1.786 1.497]
[ 2.654 3.412 1.782 1.497 1.357]]
The optimal four-bead interaction matrix in units of -RT
[[ 4.969 5.973 3.473 2.812]
[ 5.973 7.054 4.312 3.612]
[ 3.473 4.312 2.214 1.706]
[ 2.812 3.612 1.706 1.492]]
The optimal five-bead interaction matrix in units of -RT
[[ 4.969 5.973 3.739 3.113 2.593]
[ 5.973 7.054 4.625 3.932 3.357]
[ 3.739 4.625 2.647 2.099 1.723]
[ 3.113 3.932 2.099 1.758 1.440]
[ 2.593 3.357 1.723 1.440 1.249]]
Interaction matrices from Table 2 of [Abhinav]:
PAM_Koisol_2004
AGTSNQDEHRKP W YF MIVL C
[[ 1.722 3.272 3.517 3.502 2.835]
[ 3.272 5.060 5.410 5.660 4.950]
[ 3.517 5.410 5.688 5.928 4.980]
[ 3.502 5.660 5.928 6.221 5.320]
[ 2.835 4.950 4.980 5.320 5.440]]
65.1322997396
Chemical_prop
IVL FYWH KRDE GACS TMNQP
[[ 6.508 5.442 3.182 4.302 4.097]
[ 5.442 4.815 2.850 3.595 3.558]
[ 3.182 2.850 1.443 1.689 1.754]
[ 4.303 3.595 1.689 2.721 2.450]
[ 4.097 3.558 1.754 2.450 2.411]]
163.004959792
Li_2003
CFYW MLIV G PATS NHQEDRK
[[ 5.294 5.709 3.430 3.504 3.139]
[ 5.709 6.221 3.678 3.816 3.297]
[ 3.430 3.678 2.240 2.020 1.604]
[ 3.504 3.816 2.020 1.990 1.685]
[ 3.139 3.297 1.604 1.685 1.651]]
64.6189559357
WAG_Koisol_2004
AGTSNQDEHRKP CV IML FY W
[[ 1.722 2.978 3.629 3.517 3.272]
[ 2.978 5.220 5.695 5.218 5.060]
[ 3.629 5.695 6.479 6.085 5.823]
[ 3.517 5.218 6.085 5.688 5.410]
[ 3.272 5.060 5.823 5.410 5.060]]
61.9505122685
Wang_Wang_1999
CMIFLYWV AHT GP QNRSK DE
[[ 5.733 3.921 3.588 3.178 2.947]
[ 3.921 2.466 2.120 1.834 1.870]
[ 3.587 2.120 1.933 1.559 1.350]
[ 3.178 1.834 1.559 1.381 1.722]
[ 2.947 1.870 1.350 1.722 1.040]]
54.3794870699
Cieplak_2001
LFI MVWCY HA TGPRQSNED K
[[ 7.054 5.973 4.625 3.816 3.247]
[ 5.973 4.969 3.739 3.014 2.442]
[ 4.625 3.739 2.647 2.059 1.330]
[ 3.816 3.014 2.059 1.675 1.228]
[ 3.247 2.442 1.330 1.228 0.120]]
19.9558481388
Wang_Wang_2002
CMFI LVWY AGTS NQDE HPRK
[[ 6.007 5.725 3.732 3.130 3.445]
[ 5.725 5.475 3.554 3.069 3.430]
[ 3.732 3.554 2.109 1.666 1.772]
[ 3.130 3.069 1.666 1.434 1.772]
[ 3.445 3.430 1.772 1.772 1.532]]
66.2149421875