PFRMAT AL 
TARGET T0079 
AUTHOR 7278-7379-8158 
METHOD  The method is based on a combination of hidden Markov models and  
METHOD  secondary structure prediction. Each HMM represents a structural family  
METHOD  of proteins and it is trained from known secondary structure sequences  
METHOD  of proteins belonging to the structural family. 
METHOD  Secondary structure prediction is performed for the target sequence  
METHOD  using several types of prediction algorithms (GOR, QL, PHD, etc.). The  
METHOD  predicted fold of the target protein is the fold described by the HMM  
METHOD  that fits one (or most) of the predicted secondary structure sequences  
METHOD  the best. 
METHOD  At present the library consists of about 300 HMMs 
METHOD  Di Francesco et al. JMB (1997) 267, 446-463 
METHOD  Di Francesco et al. Proteins, Supplement 1 (1997) 123-128 
REMARK  Chosen models 
REMARK  1tam, a HIV matrix protein, a helical non bundle protein 
REMARK  Predator prediction without homologues was used for the alignment 
MODEL   1 
PARENT  1tam 
S       37      K     30 
G       38      L     31 
Y       39      K     32 
S       40      H     33 
K       41      I     34 
W       42      V     35 
H       43      W     36 
L       44      A     37 
Q       45      S     38 
R       46      R     39 
M       47      E     40 
F       48      L     41 
K       49      E     42 
K       50      R     43 
E       51      F     44 
T       52      A     45 
G       53      V     46 
H       54      N     47 
S       55      P     48 
L       56      G     49 
G       57      L     50 
Q       58      L     51 
Y       59      E     52 
I       60      T     53 
R       61      S     54 
S       62      E     55 
R       63      G     56 
K       64      C     57 
M       65      R     58 
T       66      Q     59 
E       67      I     60 
I       68      L     61 
A       69      G     62 
Q       70      Q     63 
K       71      L     64 
L       72      Q     65 
K       73      P     66 
E       74      S     67 
S       75      L     68 
N       76      Q     69 
E       77      T     70 
P       78      G     71 
I       79      S     72 
L       80      E     73 
Y       81      E     74 
L       82      L     75 
A       83      R     76 
E       84      S     77 
R       85      L     78 
T       93      D     96 
L       94      T     97 
T       95      K     98 
R       96      E     99 
T       97      A    100 
F       98      L    101 
K       99      D    102 
N       100     K    103 
Y       101     I    104 
F       102     E    105 
D       103     E    106 
V       104     E    107 
P       105     Q    108 
TER 
END 
