Description of Type-2 DSMs
psa-request : DSM Library : Type-2
These discrete state-space models are for either partial or
complete sequences from proteins that have one, or more, of the
following properties: they are multimeric, or multidomain, or
nonglobular, or insoluble.
There are currently two Type-2 models: a mem_span model
for membrane-spanning proteins; and a generic model for
proteins having less constrained patterns of secondary structural
elements. Having just this pair of Type-2 models is not as limiting as
it may at first appear. There are two main reasons for this.
The mem_span model is similar to the generic model
with the following exception. In addition to the helices in the generic
model, there is the additional possibility of membrane-spanning
(strongly hydrophobic) helices having lengths in the range from 18
to 24 residues inclusive. According to this model, each helix has the
probability 1/2 of being strongly hydrophobic.
- The sequence length is not a basis for analyzing proteins in a
Type-2 analysis. Therefore, each Type-2 model handles
sequences of any length.
- The generic model was intentionally constructed from a
minimal set of prior analysis assumptions. This model
is not intended to model any particular folding class. Instead,
- Each helix and each strand are modeled as equally probable
to be either buried or exposed to surrounding water
- Each tight turn is equally probable to be either two or
four residues long,
- The average lengths of strands, helices, and loops are
4.1, 9.6, 4,3 residues, respectively. Each of the length
distributions is exponential.
- The prior probabilities and expected lengths of loops,
turns, helices, and strands are consistent with a
statistical analysis of proteins of known structure.
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Last modified: Fri Sep 29 16:11:44 EDT 2000
BioMolecular Engineering Research
Boston University, Boston Massachusetts