T2: Visualizing and Accessing Structural Biology Data

Question 1

How can we describe atomic structure in 3d?

Answer 1

-internal coordinates
> only show covalent bonded structure
-external coordinates
> show all

Question 2

What info is required for 3D structures

Answer 2

Atom type
Bond type/Bonded atoms
>Angles, torsions, bond lengths
Relative position
>xyz

Question 3

What is useful for 3D atomic descriptions?

Answer 3

Library approach:
e.g. Protein Data Bank

Question 4

Visualising small molecules

Answer 4

chemdraw, sticks, ball and stick, spheres

Question 5

Visualising Proteins and what info each provides/doesnt

Answer 5

above is not really viable - too complex

Ribbon (through C-alpha atoms)
>Side chains not shown
Cartoon
>Side chains not shownb
>Coloured secondary structure (helixes)
Solvent Accessible surface
>Helps identify binding pockets