Biomedical Engineering Reference
In-Depth Information
1.1 Necessity to Predict the Protein Structure
Predicted structures can be used in structure-based drug design. It can help us
understand the effects of mutations on structure or function. Structural knowledge
brings understanding of function and mechanism of an action. It can help in pre-
diction of function.
2 Background
Protein structure is classi
ed into 4 categories [
1
]:
1. Primary structure: This structure is formed by the linear sequence of amino
acids. A single change in the amino acid sequence of hemoglobin will result in a
disease
2. Secondary structure: This structure is formed by the combination of hydrogen
bonds between amino acids from two particular elements alpha helices and beta
sheets
3. Tertiary structure: This is a more compact globular shape with carbon-rich
amino acids that is inside far away from the surrounding water
4. Quaternary structure: This structure is formed by the combination of two or
more polypeptide chains into one module with several subunits
In this paper, we are going to predict the secondary structure of a protein with
the help of two algorithms 1. DSSP and 2. GOR.
We are also visualizing that structure with the help of tools.
This kind of prediction gives us an accuracy of 70 % when compared to other
normal algorithms.
3 Methodology
The secondary structure of protein mainly constitutes of two elements: (i) alpha
helix (ii) beta sheet. The regular patterns of the H-bonds are formed between
neighboring amino acids, and the amino acids have similar
bonds.
This secondary structure has three regular forms 1. alpha helix 2. beta sheet 3.
loops. We give the input as the amino acid sequences and the results of output will
be the predicted structure. A protein consists of about 32 % alpha (
φ
and
ˈ
) helices, 21 %
↑
beta (
) sheets, and 47 % loops or non-regular structure that is it may be a motif or a
fold. In the above
↓
gure, the rotation angle around the N-c
ʱ
is called
¢
and the
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