Hello, I've recently started exploring molecular docking applications, and I'm still in the early stages. I'd like to ask Can I choose a ligand by giving the amino acid sequence and then do docking? Which applications would you suggest?
Thank you
Hello, in my experience, you must first obtain a 3D structure either de novo or by sequence construction of your peptide. I´ve tried using PepFOLD3 for structural prediction. Afterwards, you must decide which docking software you want to use, I´m familiar with Autodock and Autodock Vina, being both capable to dock small peptides, take in count that in this case, the definition of the charges in the ligands is relevant for the docking calculation. Other than that, preparation is pretty much straight forward and similar to that of the classic small ligands for docking.
Hope it helps
Hello. In order to dock a protein whose 3D structure is not available on the uniprot site, you must model its 3D structure, for this there are many servers such as Itasser, Quark, and Robetta, and after evaluating and measuring your 3D structure, you can do the docking by Servers like Cluspro, Zdock or Hdock
You need 3-D model of the ligand (peptide) as an input file for docking. You can use the sequence to build the 3-D model of peptide using molecule builder program or you can 3-D co-ordinates the atoms of the peptide molecule and optimize. The important point is that docking program perform conformational sampling of the ligand molecule by rotation around single bond in the molecule and peptide bonds are planar due to 40% partial double bond nature but shown as single bond by the modelling programs. Therefore, some restraint or constraint must be applied so that docking program do not perform rotation around peptide bond to generate wrong conformers of the peptide ligand.
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