docking2 results seem to not have contacting residues

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    • October 27, 2015 at 5:30 pm #2321
      Anonymous

        Hi, 

        I am trying to dock a predicted antibody structure onto an epitope. I don’t know the exact epitope, but I know some key residues and I’ve been using a shape complementarity server to give me a starting point before running the local docking2 protocol. I’m not getting a great “funnel” of my result files, but more importantly when I look at my structures in PyMOL there doesn’t seem to be any contacting surface area between my 2 proteins- it looks OK by eye, but all of the residues are greater than 1.4 angstroms apart. How does ROSIE define “contact” in the docking protocol when it is refining the side chains?

         

        Thanks!

      • October 31, 2015 at 9:08 pm #11299
        Anonymous

          https://en.wikipedia.org/wiki/Bond_length#Bond_lengths_in_organic_compounds

          has a chart giving covalent bond lengths up to 154 pm = 1.54 Angstroms for organic compounds.

          https://en.wikipedia.org/wiki/Hydrogen_bond#Bonding

          says “in the X−H…Y system, where the dots represent the hydrogen bond:

          the X−H distance is typically ≈110 pm, whereas the H…Y distance is ≈160 to 200 pm.”

          https://en.wikipedia.org/wiki/Disulfide#Organic_disulfides

          says “the disulfide bond is about 2.05 Å in length, about 0.5 Å longer than a C–C bond.”

          https://en.wikipedia.org/wiki/Salt_bridge_(protein_and_supramolecular)#Salt_bridges_found_in_proteins

          says “the distance between the residues participating in the salt bridge is also cited as being important.

          The distance required is less than 4 Å (400 pm). Amino acids greater than this distance do not qualify

          as forming a salt bridge.”

          Does that help?

        • November 12, 2015 at 7:29 pm #11323
          Anonymous

            Thanks AdoCbl, I think I was being a little too stringent with my cutoff. 

          • November 15, 2015 at 5:40 am #11325
            Anonymous

              I am a new user of the rosettacommons forum. Will you please tell me how to submit a new post? I cannot find the corressponding button.

               

              Smith

            • November 15, 2015 at 4:10 pm #11327
              Anonymous

                Hi Brett,

                To submit a new post, click on “New topic”  below “Home >> Forums >> ROSIE”

                and above “Topic / Topic starter” (see the image file attached below). This takes

                you to the page: https://www.rosettacommons.org/node/add/forum/99  

                I hope this helps,

                AdoCbl

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