Re: [ccp4bb] Modelling protein/protein interfaces

[Thomas Krey]

Dear all,

Thanks a lot to all of you who made helpful suggestions – I’ll look into them 
one by one.

Best wishes
Thomas



From: CCP4 bulletin board  on behalf of CHARBONNIER 
Jean-Baptiste 
Reply-To: CHARBONNIER Jean-Baptiste 
Date: Friday, February 2, 2018 at 4:18 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Modelling protein/protein interfaces

Hello
If you are dealing with oligomers conserved in evolution, InterEvDock can be a 
good choice since it implements a coevolution-based score 
(http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2).
Their new version handle oligomers with sequence alignments automatically 
generated for every subunit.
It performed very well in CAPRI.
Kind regards
JB

Laboratory of Structural Biology and Radiobiology
I2BC (Institute of Integrated Biology of the Cell)
CEA, Saclay,  Bât 144, room 140D,
91191 Gif-s-Yvette, FRANCE
phone: +33 (0)1 69 08 76 77
jb.charbonn...@cea.fr<mailto:jb.charbonn...@cea.fr>

[ccp4bb] Modelling protein/protein interfaces

[CHARBONNIER Jean-Baptiste]

Hello
If you are dealing with oligomers conserved in evolution, InterEvDock can be a 
good choice since it implements a coevolution-based score 
(http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2).
Their new version handle oligomers with sequence alignments automatically 
generated for every subunit.
It performed very well in CAPRI.
Kind regards
JB

Laboratory of Structural Biology and Radiobiology
I2BC (Institute of Integrated Biology of the Cell)
CEA, Saclay,  Bât 144, room 140D,
91191 Gif-s-Yvette, FRANCE
phone: +33 (0)1 69 08 76 77
jb.charbonn...@cea.fr

Re: [ccp4bb] Modelling protein/protein interfaces

[Maria Jose Sanchez Barrena]

I have also heard about Frodock. The primary reference:

J. I. Garzon, J. R. Lopéz-Blanco, C. Pons, J. Kovacs, R. Abagyan, J. 
Fernandez-Recio, P. Chacón (2009) FRODOCK: a new approach for fast rotational 
protein-protein docking Bioinformatics, 25, 2544-2551 

If you go to the webpage (http://chaconlab.org/modeling/frodock) you will see 
that in 2016 there was another update/release.

You can use a server as well: http://frodock.chaconlab.org/

Good luck!

Maria




El 26/01/2018, a las 14:17, Tristan Croll  escribió:

> I've been quite impressed by ClusPro (https://cluspro.bu.edu) in the past. 
> Rather than pure rigid-body docking it makes some (pretty good) effort to 
> adjust interacting sidechains into reasonable arrangements. The advanced 
> options also allow you to specify attractions and repulsions between specific 
> residue pairs so you can apply any experimental knowledge you have.
> 
> On 2018-01-26 12:34, Thomas Krey wrote:
>> Dear colleagues,
>> Is there any appropriate tool for docking an interacting protein to a
>> relatively large protein-protein interface (>2500 A2). We are facing a
>> hetero-oligomer for which we approximately know the interfaces as well
>> as the structures of the individual protomers and would like to model
>> the hetero-oligomer. I have done some small molecule docking before,
>> but the size of the interface seem to be prohibitive for using the
>> same tools in the case of such a protein-protein interaction.
>> Any help or suggestion would be highly appreciated.
>> Best wishes
>> Thomas

Re: [ccp4bb] Modelling protein/protein interfaces

[Tristan Croll]

I've been quite impressed by ClusPro (https://cluspro.bu.edu) in the 
past. Rather than pure rigid-body docking it makes some (pretty good) 
effort to adjust interacting sidechains into reasonable arrangements. 
The advanced options also allow you to specify attractions and 
repulsions between specific residue pairs so you can apply any 
experimental knowledge you have.


On 2018-01-26 12:34, Thomas Krey wrote:

Dear colleagues,

Is there any appropriate tool for docking an interacting protein to a
relatively large protein-protein interface (>2500 A2). We are facing a
hetero-oligomer for which we approximately know the interfaces as well
as the structures of the individual protomers and would like to model
the hetero-oligomer. I have done some small molecule docking before,
but the size of the interface seem to be prohibitive for using the
same tools in the case of such a protein-protein interaction.

Any help or suggestion would be highly appreciated.

Best wishes

Thomas

Re: [ccp4bb] Modelling protein/protein interfaces

[Chandra]

haddock may be an appropriate tool

https://haddock.science.uu.nl/



On 26/1/2018 8:34 PM, Thomas Krey wrote:


Dear colleagues,

Is there any appropriate tool for docking an interacting protein to a 
relatively large protein-protein interface (>2500 A2). We are facing a 
hetero-oligomer for which we approximately know the interfaces as well 
as the structures of the individual protomers and would like to model 
the hetero-oligomer. I have done some small molecule docking before, 
but the size of the interface seem to be prohibitive for using the 
same tools in the case of such a protein-protein interaction.


Any help or suggestion would be highly appreciated.

Best wishes

Thomas

[ccp4bb] Modelling protein/protein interfaces

[Thomas Krey]

Dear colleagues,

Is there any appropriate tool for docking an interacting protein to a 
relatively large protein-protein interface (>2500 A2). We are facing a 
hetero-oligomer for which we approximately know the interfaces as well as the 
structures of the individual protomers and would like to model the 
hetero-oligomer. I have done some small molecule docking before, but the size 
of the interface seem to be prohibitive for using the same tools in the case of 
such a protein-protein interaction.
Any help or suggestion would be highly appreciated.

Best wishes
Thomas