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w3DNA -- web interface to 3DNA / Binding site orientation in Composite

« on: July 12, 2020, 01:33:37 pm »

Is there any straightforward way to invert protein binding site on DNA? Since many DNA-binding protein complexes are not symmetrical, nor their recognition sequence on DNA is symmetrical, I noticed that the tool automatically interprets the 'binding site' from the reference PDB in just one of the two possible orientations. Any clue on how to select the second orientation of the binding site to make the model through Composite?

e.g.  my seq:  aaaaaaATTGGaaaaaaaaaaaGAGATaaaaaaaa  (uperrcase are the two binding sites)

     ref pdbs:        aaaATTGGaaa           aaATCTCaaa
                   protein1 (correct orientation)    protein2 (the tool selects the complementary chain as reference, so the protein is also inverted in the final model)

Thank you in advance