I am facing problems while running the peptide docking. First I tried using the peptide docking panel provided by the BioLuminate module since there is a provision in providing the peptides in the form of text. I exercised that option and I run the job though the job got completed successfully there were no ligands found. Then I tried following the normal Glide XP docking for that I need the peptides to be prepared using LigPrep but the job died due the exceed in the no.of atoms. The peptide length is of 13 and 12 residues respectively and I am unable to proceed. Please suggest what should be done? Is there a way the no.of atoms count can be increased so that the Ligprep job is done? Even though the no.of atoms are within the range 300 but the no.of rotatable bonds are many and the docking job dies.
From the manual, the peptide docking can be done provided the peptide length range is within 16. In my case it falls within that range am unable to complete the job. Please suggest what exactly I must do.
Hi Richard,
The problem that i have found with you is self explainable by the line you have said 'no.of rotatable bonds are many and the docking job dies' . So try the docking by restrict the rotatable bonds as minimum as possible. May this will help....have a good time
So how the rotatable bonds can be restricted within the limit of 50?
I have performed protein-ligand docking where in the ligand section i choose the rotational bond option which show how much restriction you allow. Similar kind of option will also present in Bioluminate. Also go on schrodinger site or youtube to check the video tutorials. One of link i am providing here: https://www.youtube.com/results?search_query=Schr%C3%B6dinger+bioluminate+Tutorials
yeah there it is I tired changing that but a pop up message was displayed telling that for that particular atom count the minimum no.of rotatable bonds to be allowed is 50 it can't go beyond that
Please try protein-protein docking e.g. by Rosetta. Preferably molecular dynamics can be used to simulate how the peptide spontaneously bind to its target protein. In general, docking software designed for drug-like small molecules are not suitable for docking a peptide of >10 residues.
Hi
I have a project like you, i use 3dDOCK, Zdock, haddock and cluspro programs, they are used for protein-protein docking frequently and are more user friendly.
Hi Richard,
For peptide docking, where you want some flexibility in the peptide, I would recommend the online flexpepdock server http://flexpepdock.furmanlab.cs.huji.ac.il/. It's based on the Rosetta framework, very easy to use, and it gave me some very reliable results in the past. Depending on how much you know about the interaction, you may want to try opposite directions of the peptide, shifting the peptide in the binding site, or alternative binding sites. Best of luck.
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