Re: [ccp4bb] protein protein interactions

[00000c2488af9525-dmarc-request]

Hello, if you mean theoretical docking, here is an old list of links:https://zlab.umassmed.edu/zdock/dockingsites.shtmlSome of these will still be maintained.Jon CooperOn 10 Feb 2020 16:50, Sarah Bowman  wrote:

Hi Careina,
 
There’s a program called FRODOCK that generates predictions of how two proteins could interact:
http://chaconlab.org/modeling/frodock
 
Cheers,
Sarah
 

Sarah EJ Bowman, PhD
 
Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center
 
Research Webpage
www.getacrystal.org


 
 

From: CCP4 bulletin board  on behalf of "careinaedgooms@yahoo.com" <02531c126adf-dmarc-request@JISCMAIL.AC.UK>
Reply-To: "careinaedgooms@yahoo.com" 
Date: Monday, February 10, 2020 at 11:17 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Fw: protein protein interactions


 



 










 









Dear all


Apologies for off topic question but can anyone recommend good programs for identifying docking interfaces between two proteins. I do not know that these two proteins
 interact. I would like a level of confidence on a possible interaction. is there a good program to do this?


kind regards


Careina













 



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Re: [ccp4bb] protein protein interactions

[Sarah Bowman]

Hi Careina,

There’s a program called FRODOCK that generates predictions of how two proteins 
could interact:
http://chaconlab.org/modeling/frodock

Cheers,
Sarah

Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center

Research Webpage
www.getacrystal.org


From: CCP4 bulletin board  on behalf of 
"careinaedgo...@yahoo.com" <02531c126adf-dmarc-requ...@jiscmail.ac.uk>
Reply-To: "careinaedgo...@yahoo.com" 
Date: Monday, February 10, 2020 at 11:17 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Fw: protein protein interactions



Dear all
Apologies for off topic question but can anyone recommend good programs for 
identifying docking interfaces between two proteins. I do not know that these 
two proteins interact. I would like a level of confidence on a possible 
interaction. is there a good program to do this?
kind regards
Careina



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Protein-Protein Interactions

[Manish Chandra Pathak]

In addition to what Francisco suggested, looking at the sequences with 
evolutionary highlited residues will provide additional info.

If modeled structures  are available , which is not the case with this query, 
investigating the corresponding electrostat potential using APBS  might give 
evidence to cross check results obtained from other method. 

Hope it helps
Manish


Manish Chandra Pathak, Ph.D. 
Indian Institute of Science Education and Research 
ITI (Gas Rahat) Building Govindpura, 
Bhopal 462023 India 
tel: +91-750-4092340


--
On Thu, Aug 2, 2012 1:28 PM EDT Francisco Hernandez-Guzman wrote:

Hi Lorenzo,

I forgot to add that any experimental data that you can provide to guide the 
modeling is highly recommended and often necessary to validate your 
predictions. Modeling can be quite useful but you should be aware of its 
strengths and weaknesses.

Cheers,

Francisco

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Francisco Hernandez-Guzman
Sent: Thursday, August 02, 2012 10:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein-Protein Interactions

Hi Lorenzo,

If the structure for your receptor is unknown, then you can use Homology 
Modeling methods to get a rough idea of the structure, MODELLER is a well know 
tool for this (http://salilab.org/modeller/). Of course depending on your % 
similarity to the template, the higher the % similarity, the more reliable 
your structure may be (of course assuming there are no major conformational 
changes, etc.)

Now, to figure out the sites of interaction, you could use a shape based 
complementarity approach like the one used in the ZDOCK algorithm 
(http://zdock.umassmed.edu/software/). This gets to be a little bit trickier 
if your % similarity to your template is low, because the dissimilarity is 
often due to surface residue differences, which are obviously the ones you're 
interested on. On the other hand, if the source of interaction is driven 
mainly by hydrophobic forces, then an analysis using the spatial aggregation 
propensity method 
(http://pubs.acs.org/doi/abs/10.1021/jp911706q?journalCode=jpcbfk) may reveal 
interesting sites of aggregation. This method is a little bit more forgiving 
that the shape complementarity one because of the intrinsic averaging that 
goes on to determine the site of aggregation.

All of these methods and other simulations tools are available in the 
Discovery Studio suite from Accelrys.

Disclaimer: I work for Accelrys as their Product Manager for the Life Science 
Modeling and Simulations suite of products. So, if you're interested in 
evaluating and gain access to these tools please contact me directly.

Kind regards,

Francisco
Sr. Product Manager
http://accelrys.com

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dr. 
Lorenzo Finci
Sent: Thursday, August 02, 2012 6:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Protein-Protein Interactions

Dear Colleagues,

I have a question for all of you bioinformatics oriented structural 
biologists: How do I predict the sites of protein-protein interactions between 
two receptors that have been proven to interact biochemically but lack 
specific details regarding proximity. This is not a straightforward question 
for me, and I believe it is somewhat complicated. The complicated scenario 
involves a multitude of different subunits and isoforms. Also, there is not 
structural data to support all components involved, and thus I presume I 
should use the sequence based software. I am aware that there are different 
types of prediction software, either sequence or structure based predictions 
using different algorithms:
http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/

Receptor 1:
-Has 5 predicted subunits (Alpha)2-(Beta)2-(Gamma)1
1. Alpha (6 isoforms)
2. Beta (3 Isoforms)
3. Gamma (3 Isoforms)

Receptor 2:
-Is believed to be composed of (Alpha)3-(Beta)2
1. Alpha (4 isoforms)
2. Beta(1 isoform)

Any advice or recommendation will be well appreciated!

Sincerely,
lorenzo
Lorenzo Ihsan FInci, Ph.D.
Postdoctoral Scientist, Wang Laboratory
Harvard Medical School
Dana-Farber Cancer Institute
Boston, MA
Peking University
The College of Life Sciences
Beijing, China

[ccp4bb] Protein-Protein Interactions

[Dr. Lorenzo Finci]

Dear Colleagues, 
I have a question for all of you bioinformatics oriented structural biologists: 
How do I predict the sites of protein-protein interactions between two 
receptors that have been proven to interact biochemically but lack specific 
details regarding proximity. This is not a straightforward question for me, and 
I believe it is somewhat complicated. The complicated scenario involves a 
multitude of different subunits and isoforms. Also, there is not structural 
data to support all components involved, and thus I presume I should use the 
sequence based software. I am aware that there are different types of 
prediction software, either sequence or structure based predictions using 
different 
algorithms:http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/Receptor
 1:-Has 5 predicted subunits (Alpha)2-(Beta)2-(Gamma)11. Alpha (6 isoforms)2. 
Beta (3 Isoforms)3. Gamma (3 Isoforms)Receptor 2:-Is believed to be composed of 
(Alpha)3-(Beta)21. Alpha (4 isoforms)2. Beta(1 isoform)Any advice or 
recommendation will be well appreciated!
Sincerely, lorenzo

Lorenzo Ihsan FInci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard 
Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityThe 
College of Life SciencesBeijing, China
  

Re: [ccp4bb] Protein-Protein Interactions

[Francisco Hernandez-Guzman]

Hi Lorenzo,

If the structure for your receptor is unknown, then you can use Homology 
Modeling methods to get a rough idea of the structure, MODELLER is a well know 
tool for this (http://salilab.org/modeller/). Of course depending on your % 
similarity to the template, the higher the % similarity, the more reliable your 
structure may be (of course assuming there are no major conformational changes, 
etc.)

Now, to figure out the sites of interaction, you could use a shape based 
complementarity approach like the one used in the ZDOCK algorithm 
(http://zdock.umassmed.edu/software/). This gets to be a little bit trickier if 
your % similarity to your template is low, because the dissimilarity is often 
due to surface residue differences, which are obviously the ones you're 
interested on. On the other hand, if the source of interaction is driven mainly 
by hydrophobic forces, then an analysis using the spatial aggregation 
propensity method 
(http://pubs.acs.org/doi/abs/10.1021/jp911706q?journalCode=jpcbfk) may reveal 
interesting sites of aggregation. This method is a little bit more forgiving 
that the shape complementarity one because of the intrinsic averaging that goes 
on to determine the site of aggregation.

All of these methods and other simulations tools are available in the Discovery 
Studio suite from Accelrys.

Disclaimer: I work for Accelrys as their Product Manager for the Life Science 
Modeling and Simulations suite of products. So, if you're interested in 
evaluating and gain access to these tools please contact me directly.

Kind regards,

Francisco
Sr. Product Manager
http://accelrys.com

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dr. 
Lorenzo Finci
Sent: Thursday, August 02, 2012 6:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Protein-Protein Interactions

Dear Colleagues,

I have a question for all of you bioinformatics oriented structural biologists: 
How do I predict the sites of protein-protein interactions between two 
receptors that have been proven to interact biochemically but lack specific 
details regarding proximity. This is not a straightforward question for me, and 
I believe it is somewhat complicated. The complicated scenario involves a 
multitude of different subunits and isoforms. Also, there is not structural 
data to support all components involved, and thus I presume I should use the 
sequence based software. I am aware that there are different types of 
prediction software, either sequence or structure based predictions using 
different algorithms:
http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/

Receptor 1:
-Has 5 predicted subunits (Alpha)2-(Beta)2-(Gamma)1
1. Alpha (6 isoforms)
2. Beta (3 Isoforms)
3. Gamma (3 Isoforms)

Receptor 2:
-Is believed to be composed of (Alpha)3-(Beta)2
1. Alpha (4 isoforms)
2. Beta(1 isoform)

Any advice or recommendation will be well appreciated!

Sincerely,
lorenzo
Lorenzo Ihsan FInci, Ph.D.
Postdoctoral Scientist, Wang Laboratory
Harvard Medical School
Dana-Farber Cancer Institute
Boston, MA
Peking University
The College of Life Sciences
Beijing, China

Re: [ccp4bb] Protein Protein interactions

[Eugene Krissinel]

Mariah,

you may want to try PISA at

http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

Eugene

On Mon, 17 Aug 2009, protein.chemist protein.chemist wrote:


Hello All,

Can anyone tell me what are the programs used to find out the different
interactions in a protein.
I am talking about both intra and intermolecular interactions.

Thanks in advance.

Mariah

Re: [ccp4bb] Protein Protein interactions

[Rotem Sertchook]

Hi,
look in our servers  list for interaction and contact analysis  
http://bip.weizmann.ac.il/toolbox/structure/tertiary.htm#contact
pay attention to PISA which is very good for intermolecular and PIC  
for intra.


Good luck
Rotem

On 17 Aug, 2009, at 20:13, protein.chemist protein.chemist wrote:


Hello All,

Can anyone tell me what are the programs used to find out the  
different interactions in a protein.

I am talking about both intra and intermolecular interactions.

Thanks in advance.

Mariah



--
Mariah Jones
Department of Biochemistry
University of Florida




Rotem Sertchook, Ph.D.
Bioinformatics Unit, Biological Services
Weizmann Institute of Science,
Rehovot 76100, Israel.

[ccp4bb] Protein Protein interactions

[protein.chemist protein.chemist]

Hello All,

Can anyone tell me what are the programs used to find out the different
interactions in a protein.
I am talking about both intra and intermolecular interactions.

Thanks in advance.

Mariah



-- 
Mariah Jones
Department of Biochemistry
University of Florida

Re: [ccp4bb] Protein Protein interactions

[Regina Kettering]

CCP4 has a program called contact where you can specify the chains, distances 
and atoms you want to explore for contacts and it will give a list of all 
contacts that fit that criteria, along with the distance.  It works best if you 
already have an idea for which chain interfaces you want to explore.  A much 
slower way is to use coot to bring up the model and look at the residue 
environments.  Again, much better if you already know which residues to use.

A better predictor for unknown interfaces would be PISA, accessible either 
directly through EMBL-EBI or indirectly through ExPASy.

Regina

--- On Mon, 8/17/09, protein.chemist protein.chemist pp73...@gmail.com wrote:

 From: protein.chemist protein.chemist pp73...@gmail.com
 Subject: [ccp4bb] Protein Protein interactions
 To: CCP4BB@JISCMAIL.AC.UK
 Date: Monday, August 17, 2009, 1:13 PM
 Hello All,
 
 Can anyone tell me what are the programs used to find out
 the different interactions in a protein.
 I am talking about both intra and intermolecular
 interactions.
 
 Thanks in advance.
 
 Mariah
 
 
 
 
 -- 
 Mariah Jones
 Department of Biochemistry
 University of Florida