Assignment 1
Protein contact map is a compact representation of three-dimensional conformations of a
protein. Prediction of the protein contact map has become one of the important prediction
tasks in protein structure prediction which is one of the challenges in the field of
bioinformatics. Prediction models have been developed to achieve better prediction of the
protein contact map that applicable to various kinds of proteins.
Table 1 shows the results of the prediction of protein contact map for 6 different proteins by
prediction model A. 2nd column of the table shows the number of true contacts that actually
appear in the proteins while the 3rd column of the table shows the total prediction made by the
prediction model A. Last, the 4th column of the table shows the number of correct predictions
of contacts from the prediction model A.
Table 1: Protein contact map prediction results for 6 proteins
Proteins
1
2
3
Number of True Contacts
95
95
225
Total Predictions
89
71
99
Number of Correct Predictions
2
12
17
In order to get further meaning from the results above, two measurements have been used by
previous researchers which are accuracy and coverage.
Ø Accuracy shows the ability of the prediction model to get correct prediction out of
total predictions.
Ø Coverage shows the ability of prediction model to identify true contacts.
Formula for accuracy and coverage is as follow:
!""#$%"& % = !"#$%& !" !"##$%& !"#$%&'%()*
! 100%
!"#$% !"#$%&'%()*
!"#$%&'$ % = !"#$%& !" !"##$%& !"#$%&'%()*
! 100%
!"#$%& !" !"#$ !"#$%&$'
Draw a flowchart and write a pseudocode for a program that runs in the following steps:
STEP 1:
STEP 2:
STEP 3:
STEP 4:
STEP 5:
STEP 6:
STEP 7:
Define 3 variables for each protein that hold data read from 2nd, 3rd and 4th columns of
Table 1 respectively from keyboard.
Define 2 variables that hold accuracy and coverage for each protein
Define variable continue_prog and assign to 1
Display a menu to let user choose whether calculate accuracy of coverage.
Ø Calculate accuracy/coverage (based on the choice on the STEP 4) for each
protein using the given formula.
Ø Display the accuracy/coverage (based on the choice on the STEP 4) for each
protein.
Ø Display a protein that has the highest accuracy/coverage (based on the choice
on the STEP 4).
Using DO WHILE loop, if continue_prog equal to 1, execute STEP 4, 5 and 6.
Ask user whether would like to use again or terminate this program. If yes, assign
continue_ prog to 1; else assign continue_ prog to 0.