text: user704: Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not? 
  If anyone has already tried such techniques I would like to hear a little brief on that subject. Which are the possible techniques, computational power needed and so on.
  
  user4306: If you have information on which part of the protein are interacting, and its sequence, you can search for homologous or similar sequences in other proteins. This would give you a list of potential targets and probably a similarity score which you can also use. Then you would have something to run simulations on. 
  And I think that with 3D structure you should be able to run simulations in silico in this case (eventhough it is probably more common to look for the ligands to the protein, not proteins to the ligand). 
  In silico simulations are computationally intensive, but I´ve also seen some being run on a laptop, so you don´t necessarily need access to HPC-clusters, or supercomputer. 
  
original_text: 704: <p>Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not? </p>
  
  <p>If anyone has already tried such techniques I would like to hear a little brief on that subject. Which are the possible techniques, computational power needed and so on.</p>
   4306: <p>If you have information on which part of the protein are interacting, and its sequence, you can search for homologous or similar sequences in other proteins. This would give you a list of potential targets and probably a similarity score which you can also use. Then you would have something to run simulations on. </p>
  
  <p>And I think that with 3D structure you should be able to run simulations <em>in silico</em> in this case (eventhough it is probably more common to look for the ligands to the protein, not proteins to the ligand). </p>
  
  <p><em>In silico</em> simulations are computationally intensive, but I´ve also seen some being run on a laptop, so you don´t necessarily need access to HPC-clusters, or supercomputer. </p>
  