Snugdock_input

Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Snugdock_input

Viewing 3 reply threads
  • Author
    Posts
    • January 19, 2017 at 12:48 am #2569
      Anonymous

        Hi

        For the input of snugdock, what if there are several chains for heavy/light chains?  For example, A and E for heavy chains and C and F for light chains?

        Do we need to merge the chains or do we change the input command line?

         

        Thank you

      • January 19, 2017 at 3:11 am #12097
        Anonymous

          How and why is your heavy or light chain multichain?  snugdock assumes standard antibodies in Chothia numbering.  If you don’t have a normal looking Fv, it’s not going to work.  If you just mean “normal looking Fv, weird stuff behind it” – just toss the other stuff out.

           

          If you want to dock multiple antibodies at once – you can’t.

        • January 19, 2017 at 3:11 am #12618
          Anonymous

            How and why is your heavy or light chain multichain?  snugdock assumes standard antibodies in Chothia numbering.  If you don’t have a normal looking Fv, it’s not going to work.  If you just mean “normal looking Fv, weird stuff behind it” – just toss the other stuff out.

             

            If you want to dock multiple antibodies at once – you can’t.

          • January 19, 2017 at 3:11 am #13139
            Anonymous

              How and why is your heavy or light chain multichain?  snugdock assumes standard antibodies in Chothia numbering.  If you don’t have a normal looking Fv, it’s not going to work.  If you just mean “normal looking Fv, weird stuff behind it” – just toss the other stuff out.

               

              If you want to dock multiple antibodies at once – you can’t.

            • January 19, 2017 at 5:04 am #12098
              Anonymous

                Is the input supposed to be Fv only? I downloaded antibody files from PDB and use it directly. Some may not be pure Fv. If that’s the case, how can I isolate the Fv part?

              • January 19, 2017 at 5:04 am #12619
                Anonymous

                  Is the input supposed to be Fv only? I downloaded antibody files from PDB and use it directly. Some may not be pure Fv. If that’s the case, how can I isolate the Fv part?

                • January 19, 2017 at 5:04 am #13140
                  Anonymous

                    Is the input supposed to be Fv only? I downloaded antibody files from PDB and use it directly. Some may not be pure Fv. If that’s the case, how can I isolate the Fv part?

                  • January 19, 2017 at 9:29 pm #12102
                    Anonymous

                      Only one “tip” of an antibody binds your target, right?  So Snugdock only works with a Fab fragment or better yet an Fv fragment – the rest of the protein is irrelevant and it’s expensive to model it.

                      Just cut away the atoms you don’t need with PyMOL (select the residues, remove the atoms, save the remaining molecule to a new file name), or by opening the PDB file up in your text editor of choice (like emacs or vi).

                    • January 19, 2017 at 9:29 pm #12623
                      Anonymous

                        Only one “tip” of an antibody binds your target, right?  So Snugdock only works with a Fab fragment or better yet an Fv fragment – the rest of the protein is irrelevant and it’s expensive to model it.

                        Just cut away the atoms you don’t need with PyMOL (select the residues, remove the atoms, save the remaining molecule to a new file name), or by opening the PDB file up in your text editor of choice (like emacs or vi).

                      • January 19, 2017 at 9:29 pm #13144
                        Anonymous

                          Only one “tip” of an antibody binds your target, right?  So Snugdock only works with a Fab fragment or better yet an Fv fragment – the rest of the protein is irrelevant and it’s expensive to model it.

                          Just cut away the atoms you don’t need with PyMOL (select the residues, remove the atoms, save the remaining molecule to a new file name), or by opening the PDB file up in your text editor of choice (like emacs or vi).

                        • January 20, 2017 at 12:42 am #12104
                          Anonymous

                            Hi here’s an example which confuses me.

                            http://www.rcsb.org/pdb/explore/explore.do?structureId=1ahw

                            There are 2 chains each for heavy and light chains. And it looks like they are all part of Fab.

                          • January 20, 2017 at 12:42 am #12625
                            Anonymous

                              Hi here’s an example which confuses me.

                              http://www.rcsb.org/pdb/explore/explore.do?structureId=1ahw

                              There are 2 chains each for heavy and light chains. And it looks like they are all part of Fab.

                            • January 20, 2017 at 12:42 am #13146
                              Anonymous

                                Hi here’s an example which confuses me.

                                http://www.rcsb.org/pdb/explore/explore.do?structureId=1ahw

                                There are 2 chains each for heavy and light chains. And it looks like they are all part of Fab.

                              • January 20, 2017 at 4:14 pm #12106
                                Anonymous

                                  IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)

                                  A, D

                                   

                                  IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)

                                  B, E

                                   

                                  TISSUE FACTOR C, F

                                   

                                  There are two copies of the whole complex in the asymmetric unit.  Fab remains two chains, as it always has…  https://en.wikipedia.org/wiki/Fragment_antigen-binding

                                • January 20, 2017 at 4:14 pm #12627
                                  Anonymous

                                    IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)

                                    A, D

                                     

                                    IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)

                                    B, E

                                     

                                    TISSUE FACTOR C, F

                                     

                                    There are two copies of the whole complex in the asymmetric unit.  Fab remains two chains, as it always has…  https://en.wikipedia.org/wiki/Fragment_antigen-binding

                                  • January 20, 2017 at 4:14 pm #13148
                                    Anonymous

                                      IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)

                                      A, D

                                       

                                      IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)

                                      B, E

                                       

                                      TISSUE FACTOR C, F

                                       

                                      There are two copies of the whole complex in the asymmetric unit.  Fab remains two chains, as it always has…  https://en.wikipedia.org/wiki/Fragment_antigen-binding

                                  • Author
                                    Posts
                                  Viewing 3 reply threads
                                  • You must be logged in to reply to this topic.