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
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Eminencegrise
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:
Are you asking about protein-DNA, protein-protein, protein-RNA or other types of docking?
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
For protein-protein interface prediction check out this link.
For the 'state of protein-protein docking' see here.
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Nir London •
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.
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You should try to better explain your problematic in order to help people providing you the solutions you are looking for.
You should try describe more specfically your problematic because, to me, it is not very clear what your question is about.
You should try describe more specifically your problematic because, to me, it is not very clear what your question is about.