How to get coil % in the predicted secondary structure of a protein

[Lilian Makgoo]

I am new to Bioinformatics and i used Phyre2 to predict secondary structure of  my protein, the output is showing the % of a-helices and Beta strands, so my question is how do I get the coil %?.

[Powell, Harry]

Hi

I don't know if there is a tool that will do that for you.

Coiled coils are made up of alpha helices, but not all alpha helices are in coils - so you have an upper limit to the percentage of coils (i.e. the percentage of helices). I think you would need to identify which residues are in coils visually (probably using a molecular graphics viewer like QTMG, Moorhen or Pymol, but there are loads out there), count them up and divide by the total (not forgetting to multiply by 100).

I hope this helps

Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
harold...@imperial.ac.uk

Phyre2 Developer
www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>


On 19/02/2025, 07:57, "ph...@googlegroups.com on behalf of Lilian Makgoo" <ph...@googlegroups.com on behalf of makgoo...@gmail.com> wrote:

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I am new to Bioinformatics and i used Phyre2 to predict secondary structure of my protein, the output is showing the % of a-helices and Beta strands, so my question is how do I get the coil %?.

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[Lilian Makgoo]

Thank you so much

[Powell, Harry]

Hi Lilian

I just found this - it may help -

Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures, Bioinformatics, Volume 37, Issue 23, December 2021, Pages 4575–4577, https://doi.org/10.1093/bioinformatics/btab631

Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
harold...@imperial.ac.uk

Phyre2 Developer
www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server>

On 19/02/2025, 10:57, "Lilian Makgoo" <makgoo...@gmail.com> wrote:

Thank you so much

On Wed, Feb 19, 2025 at 11:22 AM Powell, Harry <harold...@imperial.ac.uk> wrote:


Hi

I don't know if there is a tool that will do that for you.

Coiled coils are made up of alpha helices, but not all alpha helices are in coils - so you have an upper limit to the percentage of coils (i.e. the percentage of helices). I think you would need to identify which residues are in coils visually (probably using a molecular graphics viewer like QTMG, Moorhen or Pymol, but there are loads out there), count them up and divide by the total (not forgetting to multiply by 100).

I hope this helps

Harry Powell
—
Dr Harry Powell
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
harold...@imperial.ac.uk

Phyre2 Developer

www.imperial.ac.uk/phyre2 <http://www.imperial.ac.uk/phyre2> <http://www.imperial.ac.uk/phyre2>
Twitter for server news
twitter.com/phyre2server <http://twitter.com/phyre2server> <http://twitter.com/phyre2server>

On 19/02/2025, 07:57, "ph...@googlegroups.com on behalf of Lilian Makgoo" <ph...@googlegroups.com on behalf of makgoo...@gmail.com> wrote:

This email from makgoo...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.

I am new to Bioinformatics and i used Phyre2 to predict secondary structure of my protein, the output is showing the % of a-helices and Beta strands, so my question is how do I get the coil %?.

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[Lilian Makgoo]

Thank you so much