Table 1 The parameters used in the different model generating procedures.
From: Improving the quality of protein structure models by selecting from alignment alternatives
Model Generating Procedure | Description |
|---|---|
Arby default | Generates the default Arby models [23], exactly one for each target. Default parameters are: gap insertion 14.7, gap extension 0.37, substitution matrix Blosum62, Henikoff position-specific sequence weighting, relative weight of secondary structure is 0.24. |
PVS | Generates models resulting from alignments with parameters multiplied by a factor varying from 0.5 to 1.5 with a step width of 0.25. This results in an ensemble of alternative models for each target. |
PVH | Generates models resulting from alignments with parameters multiplied by a factor from 0.2 to 2.4 with a step width of 0.2. This results in an ensemble of alternative models for each target. |