PFRMAT AL 
TARGET T0065 
AUTHOR 5827-4749-3439 
METHOD T0065 structure prediction 
METHOD 
METHOD For this target, our HMM library showed no significant hits. 
METHOD Threading, however, suggested 1pnra1 as a potentially similar 
METHOD structure.  HMMs were then constructed which confirmed a 
METHOD weak sequence similarity. 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the  
METHOD target against all the HMMs and threading models in our libraries,  
METHOD and (2) we gathered homologs to the target using PsiBLAST,  
METHOD constructed an HMM for the target and homologs  
METHOD (using UCSC's HMM software), and scored PDB.  
METHOD This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD This target-structure prediction was primarily the result 
METHOD of agreement between the scoring of the threading models, 
METHOD and the scoring of PDB with an HMM for the target and its 
METHOD single homolog identifiable using BLAST. 
METHOD 
METHOD The alignment is automatic, produced by aligning the target 
METHOD and the structure, scop domain d1pnra1, to an HMM constructed 
METHOD for d1pnra1 and homologs. We used standard methods to create 
METHOD this HMM: (1) building an alignment using Gotoh's prrp 
METHOD software, (2) using modelfromalign from the UCSC HMM 
METHOD software to estimate an HMM from the alignment, and 
METHOD finally, (3) re-estimating this model using weights for 
METHOD the sequences to allow the HMM to generalize. The sequence 
METHOD weighting method employed used Henikoff weighting to 
METHOD establish the relative weights, and our own method of 
METHOD estimating the number of independent observations 
METHOD to establish the magnitude of the weights. 
METHOD 
METHOD The automatic alignment generated by threading agreed with 
METHOD the HMM alignment over the C-terminal half of the molecule. 
METHOD We felt that since there was an (albeit weak) sequence signal 
METHOD over the N-terminal portion as well, we decided to use the 
METHOD automatic HMM alignment. 
MODEL 1 
PARENT 1pnr_A 
M   B1    I   A4 
K   B2    K   A5 
N   B3    D   A6 
A   B4    A   A8 
K   B5    K   A9 
Q   B6    R  A10 
E   B7    A  A11 
H   B8    N  A12 
F   B9    V  A13 
E  B10    S  A14 
L  B11    T  A15 
D  B12    T  A16 
Q  B13    T  A17 
E  B14    V  A18 
W  B15    S  A19 
V  B16    H  A20 
E  B17    V  A21 
L  B18    I  A22 
M  B19    N  A23 
V  B20    K  A24 
E  B21    T  A25 
A  B25    R  A26 
N  B26    F  A27 
I  B27    V  A28 
S  B28    A  A29 
P  B29    E  A30 
E  B30    E  A31 
E  B31    T  A32 
I  B32    R  A33 
R  B33    N  A34 
K  B34    A  A35 
Y  B35    V  A36 
L  B36    W  A37 
L  B37    A  A38 
L B38    A  A39 
N  B39    I  A40 
K  B40    K  A41 
K  B41    E  A42 
S  B42    L  A43 
A  B43    H  A44 
H  B44    S  A46 
P  B45    P  A47 
G  B46    S  A48 
P  B47    A  A49 
A  B48    V  A50 
A  B49    A  A51 
R  B50    R  A52 
S  B51    S  A53 
H  B52    L  A54 
T  B53    K  A55 
V B54    V  A56 
N  B55    N  A57 
TER 
END 
