BIF401 Final Term Current Solved Papers 2022 by Muhammad Zaman

M Zaman

BIF401_Bio-informatics · Current Final Term · Questions · Full solved By M Zaman · Paper’s Collections Date From · 17-09-2022 to 22-09-2022

Improvements Of Chou Fasman Algorithm??

Special consideration for: o Nucleation regions o Membrane proteins o Hydrophobic domains o Consider variable coil and loop sizes besides the from tetra peptide turns o Consider local protein folding environments o Solvent accessibility of residues o Protein structural class o Protein’s organism M Zaman

Intra-Molecular Distance Algorithms?

o Proteins are considered as rigid bodies. o They are placed in a 3D Cartesian coordinate system. o Structural alignment in 3D. o E.g. VAST, LOCK

Inter-Molecular Distance Algorithms?

o Proteins are considered as rigid bodies. o They are placed in 2D. o Structural alignment using internal distances and angles. o E.g. DALI, and SSAP.

Fourth relationships in Jacobson Algorithm

The matrix is filled by four different positions

1. Left
2. Bottom
3. Diagonal
4. Left/Bottom elements

Expasy

It is developed by Swiss Bioinformatics Institute (SIB). Website provides access to databases and tools Proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. can be searched.

Q. How loops are found after the finding of alpha and beta sheets?

M Zaman

Tetra peptide Formula??

Answer: After computing the propensity of alpha helices and beta sheets, we need to settle for loops.

•  Let’s see how can we find out the loops using Chou Fasman Algorithm.
•  For any jth residue in sequence, we calculate f (Total) = f(j) f(j+1) f(j+2) f(j+3) (tetra peptide).

If

•  f (Total) > 0.000075.  The average value for P (turn) > 1.00 in the tetra peptide
•  The averages for the tetra peptide are such P(a-helix) < P(turn) > P(b- sheet)
•  It is a Turn!

Beta Sheets

Beta Sheets are another secondary structure that can be formed as a result of hydrogen bonding between the protein back bones. Some amino acids have a preference for making Beta Sheets. Typically, 5 to 10 resides are needed to make a Beta Strand

1. Parallel beta sheet.
2. Anti-parallel beta sheet

Beta Sheets have different Properties:

o Beta Strand