Editorial board editor-in-chief

Part of this ile was removed for brevity
2531 | 398 | 3 | D | 198 | 4 | T | 84%
2532 | 398 | 3 | D | 214 | 4 | I | 86%
2533 | 398 | 3 | D | 217 | 4 | T | 86%
2534 | 398 | 3 | D | 223 | 3 | Y | 84%
2535 | 398 | 3 | D | 274 | 6 | G | 82%
2536 | 398 | 3 | D | 276 | 4 | Q | 80%
2537 | 398 | 3 | D | 280 | 3 | K | 84%
2538 | 398 | 3 | D | 286 | 3 | Y | 82%
2539 | 398 | 3 | D | 366 | 3 | R | 86%
Computation end: 2009-06-13 12:35:58
Fig. 3.
A typical list of correlated positions

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Bioinf
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Keram: a novel stand-alone application for correlated mutations identiication and analysis
Fig. 4.
Map of the correlated mutations. The vertical and the horizontal axis represent amino acid sequence of a protein. 
The dots represent the coordinates of the sequence positions that reveal simultaneous mutations
Results
Keram has been tested in the analysis of kinase families. The 
homologous amino acid sequences were obtained from the 
Uniprot [Apweiler 
et al.
,
2004., Apweiler 
et al.
, 2004., Bairoch 
et al.
, 2005] and PFAM [Finn et al. 2006] databases. The mul
-
tiple sequence alignment was achieved with the aid of ClustalX 
[Thompson 
et al.
, 1994, Thompson 
et al.
, 1997] and reined 
with the genetic semihomology algorithm [Leluk 1998, Leluk 
2000ab, Leluk 
et al.
, 2001, Leluk 
et al.
, 2003]. For calculation 
of the distance distribution between correlated residues, the 
3D structures were taken from the Protein Data Bank [Berman 
et al.
, 2003] and ModBase [Pieper 
et al.
, 2004, Pieper 
et al
., 
2006]. The results showed serious inconsistency between the 
observed phenomenon of correlated mutations and its explanation 
by the theory of compensation. The correlated positions were 
often very distant from each other and direct or indirect mutual 
interaction was not possible. This suggests another mechanism 
of functional relationship between very distant positions that 
reveal mutational correlation. The correlation groups the related 
positions into clusters rather than pairs. The clusters may often 
consist of more than 10 positions. 
Total amount of correlated pairs:
1952|A |R |N |D |C |Q |E |G |H |I |L |K |M |F |P |S |T |W |Y |V |
A |0 |3 |4 |6 |0 |1 |3 |17 |0 |0 |14 |3 |2 |11 |6 |3 |11 |0 |1 |5 |
R |0 |1 |4 |4 |0 |2 |2 |16 |0 |0 |14 |2 |2 |11 |4 |2 |10 |0 |1 |10 |
N |0 |3 |3 |4 |0 |1 |3 |17 |0 |0 |11 |3 |1 |13 |6 |2 |11 |0 |1 |7 |
D |0 |3 |6 |4 |0 |2 |3 |17 |0 |0 |14 |3 |3 |13 |6 |3 |14 |0 |2 |8 |
C |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |
Q |0 |2 |2 |4 |0 |0 |2 |8 |0 |0 |2 |2 |1 |6 |4 |2 |6 |0 |0 |3 |
E |0 |2 |3 |3 |0 |1 |1 |11 |0 |0 |8 |2 |1 |9 |4 |1 |7 |0 |1 |5 |
G |0 |9 |14 |14 |0 |4 |8 |41 |0 |0 |44 |9 |5 |36 |16 |8 |33 |0 |4 |27 |
H |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |
I |0 |1 |2 |2 |0 |0 |1 |5 |0 |0 |5 |1 |1 |5 |2 |1 |5 |0 |1 |3 |
L |0 |10 |12 |11 |0 |1 |10 |51 |0 |0 |35 |10 |7 |37 |19 |6 |33 |0 |3 |22 |
K |0 |2 |4 |4 |0 |2 |2 |14 |0 |0 |14 |1 |2 |11 |4 |2 |10 |0 |2 |10 |
M |0 |1 |1 |2 |0 |1 |1 |5 |0 |0 |6 |1 |0 |4 |2 |1 |5 |0 |1 |2 |
F |0 |6 |10 |9 |0 |3 |6 |32 |0 |0 |30 |6 |4 |20 |11 |5 |21 |0 |3 |18 |
P |0 |2 |4 |4 |0 |2 |2 |14 |0 |0 |14 |2 |2 |11 |2 |2 |10 |0 |2 |9 |
S |0 |2 |3 |2 |0 |1 |2 |11 |0 |0 |6 |2 |1 |7 |4 |0 |7 |0 |1 |5 |
T |0 |7 |12 |14 |0 |2 |7 |40 |0 |0 |37 |7 |6 |29 |14 |7 |27 |0 |6 |24 |
W |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |0 |
Y |0 |3 |4 |6 |0 |2 |3 |15 |0 |0 |16 |3 |3 |12 |6 |3 |15 |0 |2 |8 |
V |0 |6 |6 |6 |0 |1 |4 |26 |0 |0 |19 |6 |2 |18 |9 |4 |18 |0 |1 |10 |
Fig. 5.
Correlated mutations distribution within all 400 possible amino acid pairs calculated by Keram

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Bioinf
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