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What tools are available to predict, based on the structure of a certain protein, its interactions within a cell?

For example, I am considering the split GFP protein and I am trying to predict if there will be any interactions which might hinder its binding efficiency to the other half of the GFP protein.

Note that I am not only looking for protein interactions, but other molecules as well.

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You could try one of these tools to predict protein-protein interactions:

  1. Struct2Net

    Given two protein sequences, the structure-based interaction prediction technique threads these two sequences to all the protein complexes in the PDB and then chooses the best potential match. Based on this match, the method generates alignment scores, z-scores, and an interfacial energy for the sequence pair. Logistic regression is then used to evaluate whether a set of scores corresponds to an interaction or not. The algorithm is also extended to find all potential partners given a single protein sequence. Further details about the method are described here.

  2. PRED

    Pred_PPI is a web-based system that serves for predicting PPIs from different organisms. This server is freely available to any researcher wishing to use it for non-commercial purposes. Based on auto covariance (AC) and support vector machine (SVM), this tool is capable of predicting PPIs for any target protein pair only using their primary sequences, and assigning an interaction probability to each SVM prediction as well. So the user can use this tool to predict novel PPIs with high confidence.

For protein-RNA interactions, you can try:

  1. catRapid

    Through the calculation of secondary structure, hydrogen bonding and van der Waals contributions, catRAPID is able predict protein-RNA interaction propensities with great accuracy (up to 89% on the ncRNA-protein interaction database, NPinter).

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  • $\begingroup$ See updated question, the OP ist not only looking for Protein-Protein interactions... $\endgroup$
    – llrs
    Jun 27 '17 at 15:50
  • $\begingroup$ @Llopis ah, damn. That will be harder. $\endgroup$
    – terdon
    Jun 27 '17 at 16:13
  • $\begingroup$ Thank you for the original answer this does help though $\endgroup$
    – jaslibra
    Jun 28 '17 at 12:13
  • $\begingroup$ @jaslibra catRapid should be good too. I haven't used it but have used other tools by the same author and they tend to be very good. What else do you need though? Protein-protein and protein-RNA, and what else? $\endgroup$
    – terdon
    Jun 28 '17 at 12:17
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IBIS reports protein interaction with other biomolecules. Your protein or homolog must exist in the Protein Data Bank.

IBIS @ NCBI: https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi

"For a given protein sequence or structure query, IBIS reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation."

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