Structure analyses

With the knowledge from the functional predictions from the previous section you can look closer at physical/evolutionary properties of your protein. Molecular function is dictated by the physical properties of particular amino acids in your protein and the analysis of commonalities (differences) within your protein family or with other protein structures often indicate functional similarities (differences). For example, analyse the following properties visually:

• putative pockets in the structure

to be added

• electrostatic surface potential

Use the [APBS tool in PyMOL] and visualise the surface as explained in the brief PyMOL tutorial

• residue conservation

Scorecons

• surface similarities

Computed atlas of surface topography of proteins CASTp

Discuss these results in the context of putative functions and illustrate putative functional residues (sites) also in the multiple sequence alignment from section 3.

--ThomasHuber 17:32, 25 April 2007 (EST)