Hydrophobicity and similar values

kun_rodrigues_celia · 5 January 2016 16:36

Dear Jalview Administrator,

If, given a pdb file, could Jalview give me average values of hydrophobicity, polarity, maybe propensity to be buried or to form helix, or maybe even surface or active centre accessibility for the whole protein structure? I just want one value for the whole structure.

Thank you,

Celia

g_m_carstairs · 6 January 2016 12:04

Hello Celia,

The short answer is no - Jalview does not compute values for these properties, so has no data that could be averaged over the structure for them.

Jalview does have built-in sequence colour schemes for hydrophobicity, helix propensity, and buried index (see http://www.jalview.org/help/html/colourSchemes/index.html), but these are based only on the amino acid residues (a global average), not on their context in the specific structure.

Dedicated structure viewers (Jalview supports integration with Chimera and Jmol) may have some capability to provide what you are after, but I will have to leave that to others more expert in those tools to comment on .

Best regards,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Kun Rodrigues, Celia celia.rodrigues@ucl.ac.uk
Sent: 05 January 2016 16:36
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Hydrophobicity and similar values

Dear Jalview Administrator,

If, given a pdb file, could Jalview give me average values of hydrophobicity, polarity, maybe propensity to be buried or to form helix, or maybe even surface or active centre accessibility for the whole protein structure? I just want one value for the whole structure.

Thank you,

Celia

geoff.barton · 6 January 2016 12:12

As Mungo says, Jalview provides a variety of ways to calculate properties from sequences (that could be read in from a PDB file) but does not provide an overall average. There are some overall properties calculated from sequences available from the expasy.ch website that might do what you want. In addition, our TarO server (See www.compbio.dundee.ac.uk for links) will also calculate properties given a single sequence (e.g. GRAVY and predicted pI). Again, these are just from the sequence and take no account of the structural environment of the amino acids.

I hope this helps.

Geoff.

···

On 06/01/2016 12:04, Mungo Carstairs (Staff) wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096

elaine_c_meng · 6 January 2016 17:17

Hi Celia,
Chimera could calculate average Kyte-Doolittle hydrophobicity of the amino acid residues in a structure (ignoring the other residues like water) with only a few steps. To use a different amino acid hydrophobicity scale or calculate the other things you mention would be a lot more complicated. There isn’t helix propensity but you can calculate surface areas.

For the hydrophobicity, you’d just open the structure, then choose “Tools… Structure Analysis… Attribute Calculator” from the menu. In the resulting dialog, calculate attribute [whatever-name-you-want] for [molecules] with formula:

average(residue.kdHydrophobicity)

click Apply. I hope this isn’t too off-topic for the list,
Elaine

···

-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 6, 2016, at 4:12 AM, Geoff Barton <gjbarton@dundee.ac.uk> wrote:

As Mungo says, Jalview provides a variety of ways to calculate properties from **sequences** (that could be read in from a PDB file) but does not provide an overall average. There are some overall properties calculated from sequences available from the expasy.chwebsite that might do what you want. In addition, our TarO server (See www.compbio.dundee.ac.uk for links) will also calculate properties given a single sequence (e.g. GRAVY and predicted pI). Again, these are just from the sequence and take no account of the structural environment of the amino acids.

I hope this helps.

Geoff.

On 06/01/2016 12:04, Mungo Carstairs (Staff) wrote:

Hello Celia,

The short answer is no - Jalview does not compute values for these properties, so has no data that could be averaged over the structure for them.

Jalview does have built-in sequence colour schemes for hydrophobicity, helix propensity, and buried index (see http://www.jalview.org/help/html/colourSchemes/index.html), but these are based only on the amino acid residues (a global average), not on their context in the specific structure.

Dedicated structure viewers (Jalview supports integration with Chimera and Jmol) may have some capability to provide what you are after, but I will have to leave that to others more expert in those tools to comment on<Mail Attachment.png>.

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Kun Rodrigues, Celia<celia.rodrigues@ucl.ac.uk>
Sent: 05 January 2016 16:36
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Hydrophobicity and similar values

Dear Jalview Administrator,

If, given a pdb file, could Jalview give me average values of hydrophobicity, polarity, maybe propensity to be buried or to form helix, or maybe even surface or active centre accessibility for the whole protein structure? I just want one value for the whole structure.

Thank you,
Celia

kun_rodrigues_celia · 7 January 2016 11:10

Dear all,

Thank you all for your suggestions.
This is a useful discussion board.

Dear Elaine, I came accross Chimera before and it seemed it could give me one or two of the things I wanted to calculate. I will follow your advice. That's exactly what I was looking for.

Best regards,
Celia

···

________________________________________
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: 06 January 2016 17:17
To: Kun Rodrigues, Celia
Cc: gjbarton@dundee.ac.uk; Mungo Carstairs (Staff); jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Hydrophobicity and similar values

Hi Celia,
Chimera could calculate average Kyte-Doolittle hydrophobicity of the amino acid residues in a structure (ignoring the other residues like water) with only a few steps. To use a different amino acid hydrophobicity scale or calculate the other things you mention would be a lot more complicated. There isn’t helix propensity but you can calculate surface areas.

For the hydrophobicity, you’d just open the structure, then choose “Tools… Structure Analysis… Attribute Calculator” from the menu. In the resulting dialog, calculate attribute [whatever-name-you-want] for [molecules] with formula:

average(residue.kdHydrophobicity)

click Apply. I hope this isn’t too off-topic for the list,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 6, 2016, at 4:12 AM, Geoff Barton <gjbarton@dundee.ac.uk> wrote:

As Mungo says, Jalview provides a variety of ways to calculate properties from **sequences** (that could be read in from a PDB file) but does not provide an overall average. There are some overall properties calculated from sequences available from the expasy.chwebsite that might do what you want. In addition, our TarO server (See www.compbio.dundee.ac.uk for links) will also calculate properties given a single sequence (e.g. GRAVY and predicted pI). Again, these are just from the sequence and take no account of the structural environment of the amino acids.

I hope this helps.

Geoff.

On 06/01/2016 12:04, Mungo Carstairs (Staff) wrote:

Hello Celia,

The short answer is no - Jalview does not compute values for these properties, so has no data that could be averaged over the structure for them.

Jalview does have built-in sequence colour schemes for hydrophobicity, helix propensity, and buried index (see http://www.jalview.org/help/html/colourSchemes/index.html), but these are based only on the amino acid residues (a global average), not on their context in the specific structure.

Dedicated structure viewers (Jalview supports integration with Chimera and Jmol) may have some capability to provide what you are after, but I will have to leave that to others more expert in those tools to comment on<Mail Attachment.png>.

Best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Kun Rodrigues, Celia<celia.rodrigues@ucl.ac.uk>
Sent: 05 January 2016 16:36
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Hydrophobicity and similar values

Dear Jalview Administrator,

If, given a pdb file, could Jalview give me average values of hydrophobicity, polarity, maybe propensity to be buried or to form helix, or maybe even surface or active centre accessibility for the whole protein structure? I just want one value for the whole structure.

Thank you,
Celia