Protein MSA secondary structure

I needed to predict the secondary structure of amino acid sequences, already in a multiple sequence alignment (MSA). This means that the sequences had gaps, which could be a problem. I searched the net for a suitable, easy-to-use application or online server. Read the rest of this entry »

UCSF Chimera and Firefox

I’ve been doing some protein structure modelling using the amazing PHYRE2. Viewing the results summary in Firefox shows a list of models with thumbnails. Clicking on a thumbnail links to the corresponding PDB file and by default the browser will display it either as text or will ask you to download the PDB file. Read the rest of this entry »