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Table 4 SABERTOOTH Alignment Parameters

From: SABERTOOTH: protein structural alignment based on a vectorial structure representation

Parameter

EC

revised PE

p align,exp

1.60

1.79

p break,fac

1.79

3.25

p break,exp

1.57

0.38

p break,term,exp

  

p insert,fac

0.43

0.83

p insert,term,fac

0.31

0.58

p insert,exp

p insert,term,exp

1.77

0.89

  1. Penalties for alignment of positions, breaking a protein chain and for inserting a chain fragment opposite to a gap. The same parameter values are used in the profile alignment as well as in the refinement routine. Please refer to UB, A.R.Ortíz, MP, FT: Effective Connectivity: A structural profile for multi-domain proteins, submitted, for the definition of the EC profile and to [10] for the revised PE.
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BMC Bioinformatics

ISSN: 1471-2105

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