Hi Larry, My guess is that you need a docking tool (like DOCKTHOR server; https://dockthor.lncc.br/v2/).
So you pulled the protein structures from the web... the coordinates from one is arbitrary to the other. If they interact in a way that forms a protein-protein interface (PPI) then you need a PPI docking software also to get the complex. But my guess is that you don't need the complex and the small ligand will bind to only one of the proteins... I don't know. Hope it helps, Abraços, Em seg., 6 de jul. de 2020 às 15:09, Larry Mahan <digr...@gmail.com> escreveu: > Hello, > Like others, I am new to Pymol. I am interested in seeing if a small > molecule (.mol2) "ligand" has a binding site on one of two proteins (2KAV > and 5FEB) but since they are known to interact, it might be something > between the two. While I am also looking into/learning Autodock Vina, in > Pymol I tried pulling up one protein (successful), then the other > (successful) and interestingly they came up somewhat "intertwined" next to > each other. Then I brought in the small molecule (300MW) and it jumped to > an orientation with one end next to an a.a. of one protein and the other > end next to an a.a. of the other. And some of the side groups made possible > sense (e.g. H-bonding). No matter which order I pull up the proteins or > molecule, they always configure this same way. > > So my question is ... are these alignments just fortuitous? (then why the > same each permutation of adding) or is Pymol suggesting an optimal > alignment for the 2 proteins and "suggesting" a binding site for the small > molecule? > Is there a better way to look at this? > Thanks for any insights! > > Larry (pymol newbie) > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Pedro Sousa Lacerda Laboratório de Bioinformática e Modelagem Molecular Faculdade de Farmácia / UFBA @pslacerda +55 71 9 9981-1856 http://lattes.cnpq.br/8338596525330907
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