Hydrogen bond detection and shape complementarity

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Hydrogen bond detection and shape complementarity

Viewing 2 reply threads
  • Author
    Posts
    • June 14, 2019 at 9:39 am #3177
      Anonymous

        HI,

        I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line

        report_hbonds_for _plugin.linuxgccrelease

        -s

        -prevent packing true

        sc.linuxgccrelease

        however the command is not functioning in my rosetta installation.i can run other command line for docking but not the above mentioned command. Please any one let me know its precise location in the rosetta folder so that i can set env path in the ~/.BASHRC FILE.

        Anticipating a response soon

        Suji george

        National institute of Virology,

        Pune, india

         

      • June 14, 2019 at 5:16 pm #14774
        Anonymous

          It looks like both of these apps are pilot apps, and should have been moved to public apps upon publication.  I’ll open a PR to move these into public apps and they will be in the next weekly release of Rosetta.

          • June 15, 2019 at 4:11 am #14775
            Anonymous

              Thank you very much for the prompt response

              regards 

              Suji George 

          • June 27, 2019 at 8:30 am #14807
            Anonymous

               

               Hi,

              I have found  an alternative to the above mentioned  report_hbonds_for _plugin.linuxgccrelease and sc.linuxgccrelease. The Interfaceanalyser does the job of reporting the shape complimentarity and hydrogen bond parameters. The interfaceanalyser also reports the pymol selection of the residues. However is there a way to get detailed output report of the residue and atom involved in the hydrogen bond, something similar to the program HBPLUS. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456)  the results from the HBPLUS and report_hbonds_for _plugin.linuxgccrelease are similar. Similarly is it possible with Interfaceanalyser to report the residue and atom involved in the hydrogen bond of the interface of the complex. 

              With Regards

              Dr. Suji george 

          • Author
            Posts
          Viewing 2 reply threads
          • You must be logged in to reply to this topic.