fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
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Get volume of a single tunnel in several similar proteins and limit tunnel length outwards #149
First of all, I apologize if this is not the proper place to ask usage questions.
Now, to the questions:
I have several structurally similar proteins (wild-types) and I am interested in measuring the volume of a particular tunnel in these proteins in order to evaluate their capacity to accommodate a certain ligand. What is the recommended way to automate this task? I was thinking about aligning all structures to one with the ligand, save the structures with a copy of the ligand, and then use dpocket on a .txt input file containing the line "/workdir/protein_lig_complex.pdb LIG" for each complex. When I tested this, the first pocket identified was indeed the one of interest, but dozens of other pockets that I am not interested in were also identified. That leads to my second question:
When focusing on one ligand with dpocket, is there a way to turn off the identification of other pockets?
Now, I'm mostly interested in the volume on the dead end of the tunnel because this is where I hypothesize that the specificity for a longer ligand is controlled. I want the tunnel to stop being computed at a fixed position before it reaches the exit of the tunnel. That is because the volume variation in this region may introduce noise to the analysis. Hence, my question is: how to limit how "far" the tunnel will be computed towards the exit, supposing that it starts on its dead end? I've tried using for instance
fpocket -f /workdir/complex.pdb -P 89::A.148::A.156::A.157::A.247::A.288::A.318::A.319::A.348::A.350::A.378::A.64::B
but I get
! No pocket to refine! (argument NULL: (nil)).
no pockets found
I've also tried
fpocket -f /workdir/complex.pdb -r 393:LIG:H
And it worked. It identified only the pocket of interest. However, it also identified several regions outside the tunnel of interest as a pocket (the ligand is long and is partly solvent-exposed. Can I limit this using an option during the run, or will -r always have priority over those options? I've tried reducing -D, but it didn't change the results.
Hi all,
First of all, I apologize if this is not the proper place to ask usage questions.
Now, to the questions:
fpocket -f /workdir/complex.pdb -P 89::A.148::A.156::A.157::A.247::A.288::A.318::A.319::A.348::A.350::A.378::A.64::Bbut I getfpocket -f /workdir/complex.pdb -r 393:LIG:HAnd it worked. It identified only the pocket of interest. However, it also identified several regions outside the tunnel of interest as a pocket (the ligand is long and is partly solvent-exposed. Can I limit this using an option during the run, or will -r always have priority over those options? I've tried reducing -D, but it didn't change the results.Thank you in advance!
P.S.: I'm running fpocket on Docker on Windows.