INDEXING and MAPPING of PROTEINS by SAMMON'S PROJECTION ALGORITHM
By: Izydor Apostol (Baxter Inc.), Wojciech Szpankowski
A modified Sammon algorithm is developed to display a relationship
between proteins based on their amino acid composition. In the first stage
of the method, a 19-dimensional compositional space of representative
proteins was mapped into a 2-dimensional space (2-D) using the
original Sammon projection creating a contour map.
In the second stage, this contour map was used as a reference for
new proteins projected into 2-D. Data analysis showed that proteins
belonging to the same structural classes formed characteristic and
distinct clusters, which could be potentially useful in the prediction
of protein structural classes. However, we observed significant overlapping
of the clusters which may explain the limited success of previous
protein folding prediction based solely on amino acid composition.
Regardless, the modified Sammon projections can generate a unique
index for each individually projected protein related to its
amino acid composition, which
may be a useful tool in the exploratory classification of proteins.
The method and results are describe din details in our paper:
I. Apostol and W. Szpankowski,
Indexing and Mapping of Proteins Using a Modified Nonlinear Sammon's
Projection, (pdf format)
Journal of Computational Chemistry, June 1999.
In addition, if one wants to run the program that we used to produce our results, click here to download sammon.zip file. You must unzip before using it.