Tools to analyze/relate protein structural information to its 3D information

Question

[ishengomae]

Hi all.

Please I'm doing certain evolutionary analysis using Ziheng Yang's PAML/codeml and normally the tool will predict certain amino acid residues to be 'positively selected sites'. Now which tool will help me take these positive sites and then visualize their relationships to the three dimensional shape of the proteins (proximity to active sites, proteins domains, etc)?

Thanks.

Answer 1

[a.polo88]

depend if you have already the information about whis is the active sites, protein domain ect, than you can use Jmol to visualize the protein in a grapich way. but there is Pfam for protein domain, Ligplot+ to visualize which aa residues interact with the active sites and other tools