Question: Do You Know Of Any Tools For Inference Of Docking Sites In Plants?
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gravatar for Eminencegrise
8.7 years ago by
Eminencegrise210
Eminencegrise210 wrote:

I would be grateful if people that have worked with that problem per se could direct me to tested and used software and reasonable papers

docking • 1.9k views
ADD COMMENTlink written 8.7 years ago by Eminencegrise210

You should try to better explain your problematic in order to help people providing you the solutions you are looking for.

ADD REPLYlink written 8.7 years ago by Fred Fleche4.3k

You should try describe more specfically your problematic because, to me, it is not very clear what your question is about.

ADD REPLYlink written 8.7 years ago by Fred Fleche4.3k

You should try describe more specifically your problematic because, to me, it is not very clear what your question is about.

ADD REPLYlink written 8.7 years ago by Fred Fleche4.3k
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gravatar for Khader Shameer
8.7 years ago by
Manhattan, NY
Khader Shameer18k wrote:

From my experience you may define docking sites in 3D structures using knowledge based approaches or de-novo approaches. Knowledge based approach is based on available literature information and it can help you to identify functional sites reported from experimental studies. You may use this information and use in protein-protein docking tools as the location for your docking. Other option is to use the binding site prediction tools or allow the docking software (for example AutoDock can find probable binding pockets) to identify the binding sites. I have evaluated a variety of docking protein-protein docking tools and I found better results with ZDOCK.

Various algorithms are available for finding the binding sites: For finding binding site based on conservation you may Consurf . Other option is SiteFinder3D which uses a different approach for identifying functional sites. Since you are working specifically with Protein-Protein complexes you may also try the Pepsite which is a structural method to predict peptide/protein binding. If you want to mine individual interactome of your protein of interest to find interesting functional patterns of peptides for docking studies you may use PeptideMine (Disclaimer: PeptideMine is developed as a part of my PhD)

Additional reading:

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Khader Shameer18k
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gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Are you asking about protein-DNA, protein-protein, protein-RNA or other types of docking?

ADD COMMENTlink written 8.7 years ago by Larry_Parnell16k

protein protein docking interactions, I am trying to predict docking sites from a set of sequences with MSA, I am not sure whether I should go ahead and mask out certain parts of the sequence

ADD REPLYlink written 8.7 years ago by Eminencegrise210
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gravatar for Nir London
8.7 years ago by
Nir London220
Nir London220 wrote:

For protein-protein interface prediction check-out: http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/ For the 'state of protein-protein docking' see: http://rosettadesigngroup.com/blog/535/capri-state-of-protein-protein-docking/

ADD COMMENTlink written 8.7 years ago by Nir London220
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gravatar for ilovepython
8.4 years ago by
ilovepython130
ilovepython130 wrote:

My experience with the auto* suite of software has been great! Autoligand can be used to find potential binding sites. Then autogrow can provide in silico fragment based ligand discovery.

ADD COMMENTlink written 8.4 years ago by ilovepython130
0
gravatar for Ckin
7.6 years ago by
Ckin0
Ckin0 wrote:

have any of you have tried ptools? can someone explain what is the differences of this tool compared to above mentioned tools? Thanks!

ADD COMMENTlink written 7.6 years ago by Ckin0
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