MBA:
Model-Based Assignment


A software for inferential assignment of protein
backbone nuclear magnetic resonances

 

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Installation

Input files

Execution

Output

Convergence

Output:

The MBA output file is mba.out. It contains a description of input parameters, individual mappings, a summary of all the mappings found, and a comparison to the reference solution of it is present.

 

The output file starts with a description of execution parameters that are given in the input file, or specified internally within the program. Here is an example: 

Match tolerance CO = 0.25
Match tolerance CA = 0.5
Match tolerance CB = 0.5
Match tolerance HA = 0.25

..............................................

 

The description of the parameters is followed by a description of the protein: 

PROTEIN:
========
Name: ubiq_cs.tab
Number residues: 76
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

..............................................

 

If a reference mapping is present, it is described next. The description shows number of pseudoresidues, penalized likelihood on the -2log scale, ids of pseudoresidues in the reference order, and inconsistent pairs of pseudoresidues. The pairs are inconsistent if their chemical shifts do not agree with the predicted distribution for the amino acid type, or if the match difference exceeds the tolerance level. 

REFERENCE MAPPING:
==================
Missing pseudoresidues:     2; Penalized -2log(Likel):    469.2
 -, 2, 3, 4, 5, 6, 7, 8, 9,10,11,12,13,14,15,16,17,18, P,20,21,22,23,Mis,25,26,27,28,29,30,31,32,
33,34,35,36, P, P,39,40,41,42,43,44,45,46,47,48,49,50,51,52,Mis,54,55,56,57,58,59,60,61,62,63,64,
65,66,67,68,69,70,71,72,73,74,75,76,
Inconsistent pairs:
None

 

Next the output file enumerates all the globally consistent mappings that were found. 

 29 INDIVIDUAL MAPPINGS:

Missing pseudoresidues:     4; Penalized -2log(Likel):    460.6
 -, 2, 3, 4, 5, 6, 7, 8, 9,10,11,12,13,14,15,16,17,18, P,20,21,22,23,Mis,25,26,27,28,29,30,31,32,
33,34,35,36, P, P,39,40,41,42,43,44,45,46,47,48,49,50,51,Mis,Mis,54,55,56,57,58,59,60,61,62,63,64
,65,66,67,68,69,70,71,72,73,74,75,Mis,

..............................................

 

The description is followed by a summary of the individual mappings. All mapped pseudoresidues are written next to the corresponding positions in the sequence. Mis indicates a possibility of a missing pseudoresidue. (H) indicates pseudoresidues mapped with high confidence. 

SUMMARY OF 29 INDIVIDUAL MAPPINGS:

Pos * pseudo residues.

M  [  1]           
Q  [  2]     (H)   PR_2 
I  [  3]     (H)   PR_3 
F  [  4]     (H)   PR_4 
V  [  5]     (H)   PR_5 
K  [  6]     (H)   PR_6 
T  [  7]     (H)   PR_7 
L  [  8]     (H)   PR_8 
T  [  9]     (H)   PR_9 
G  [ 10]     (H)   PR_10 
K  [ 11]     (H)   PR_11 
T  [ 12]     (H)   PR_12 
I  [ 13]     (H)   PR_13 
T  [ 14]     (H)   PR_14 
L  [ 15]     (H)   PR_15 
E  [ 16]     (H)   PR_16 
V  [ 17]     (H)   PR_17 
E  [ 18]     (H)   PR_18 
P  [ 19]           
S  [ 20]     (H)   PR_20 

..............................................

G  [ 35]     (H)   PR_35 
I  [ 36]     (H)   PR_36 
P  [ 37]           
P  [ 38]           
D  [ 39]     (H)   PR_39 
Q  [ 40]     (H)   PR_40 
Q  [ 41]     (H)   PR_41 
R  [ 42]     (H)   PR_42 
L  [ 43]     (H)   PR_43 
I  [ 44]     (H)   PR_44 
F  [ 45]     (H)   PR_45 
A  [ 46]     (H)   PR_46 
G  [ 47]     (H)   PR_47 
K  [ 48]     (H)   PR_48 
Q  [ 49]     (H)   PR_49 
L  [ 50]     (H)   PR_50 
E  [ 51]           PR_51 Mis
D  [ 52]           PR_52 PR_69 Mis
G  [ 53]           
R  [ 54]     (H)   PR_54 
T  [ 55]     (H)   PR_55 
L  [ 56]     (H)   PR_56 
S  [ 57]     (H)   PR_57 

..............................................

 

The last line of the file summarises the detected mappings and the compares the results to the reference mapping. Below is an example of the last line: 

SUMMARY STATISTICS:
        Length         AssignablePos    BestScore         Error        RefMiss
 Protein      Mappings            Reliable       RefScore     BestMiss       Idle
    ubiq    76      29      70       65   460.6    469.2    0       4      2  248
The fields are:
Protein: the name of the protein.
Length: the number of residues.
AssignablePos: the number of residues minus the number of Prolines and the first residue.
Reliable: the number of reliably assigned residues.
BestScore: the highest posterior probability on the -2log scale. Maximizing the posterior probability is equivalent to minimizing the score.
RefScore: the score of the reference mapping if a reference mapping is provided.
Error: the number of residues with assignments that disagree with the reference solution.
BestMiss: the number of missing pseudoresidues in the reference mapping.
RefMiss: the number of pseudoresidues in the reference mapping.
Idle: the number of iterations that did not produce an improvement.