SOPMA
(Self Optimised prediction Method with Alignments)
Every protein achieve the secondary structures determined by the nature of the amino acids present in
the given protein sequences . For any given protein , bioinformatics provides a tool to predict the
secondary structure protein in form of alpha helix , beta pleated, loop , turn etc. Infact the structure is
determined by the rotation around phi and psi angle formed on the either side of peptide bond.
Prediction of secondary structure of newly discovered protein is essential as it forms motif sand domain
at which the intermolecular interaction takes place. Even every function and structural protein needs a
particular of specific structure. Before any one wants to modify any protein its prior knowledge of
secondary structure is required Bioinformatics provides a very significant domain to users to analyse the
secondary structure of huge protein sequence apart from their percentage which are displayed as
output.
SOPMA(Self Optimised prediction Method with Alignments) is such tool which is based on the
homologue method of Levin et al, (1986)). The improvement takes place because SOPMA take into
account the information from an alignment of sequences belonging to the same family It takes several
minutes to compute larger sequences (>500 amino acids). This method can be accessed via NPSA( Net
work protein sequence analyser) through sever www.npsapbil.ibcp.fr/.)
If the user enters an unknown protein sequence , it will search against a collection of related
proteins in the database that have some similar properties and evolutionary history.
Procedure /Steps
Open the SOPMA home page by simply login sever www.npsapbil.ibcp.fr/
Enter the input protein sequence in text ,if fasta sign is thee , remove this sequence in the space
provided
Click Submit button
Secondary structure result appears
Input box
Home page of SOPMA
Result will appear like this as displayed below
As shown here first line is protein sequence displayed in single alphabet representation
Below this sequence length is given for example here it is 212
Second line represent the different secondary structure pertain to specific regions like
e- Extended strand
Gg 310 helix
Bb Beta turn
Hh alpha helix Ss bend region etc Beside this number of amino acids involve is given and then
percentage of the particular structure formed
Below this bar diagram is represented
And lastly graphical representation is displayed . every representation is distinguished bt different
colour.
Thus it is a very important tool to predict the secondary structure of protein
