Lecture 1

Question 1

When are two proteins homologous?

Answer 1

Share the same common ancestor.

Question 2

Name three things you need for sequence sequence info?

Answer 2

Sequence searching

Sequence alignment

Domain alignment

Phylogenetic tree

Question 3

Sequence structure?

Answer 3

Homologous modelling

Fold assignment

Functional site id

Question 4

Structure structure?

Answer 4

Functional sites

Binding sites

Docking

Question 5

What is the twilight zone?

Answer 5

Below 20-35% sequence identity proteins will not share same fold

• chance of observing 30% identity between non-homologous proteins is small due to size of random sequence space.
• quality of pairwise sequence alignments falls below 30% –> assignment errors and structural distortions in model building.