Here are the slides from my talk "Drug Design and pH" that I'll give in Thursday (February 10) as part of the Ph.D. course Biostructure and Molecular Modelign in Drug Research over at the Faculty of Pharmacy.
I went to the Ph.D. course two weeks ago - thank you for an interesting talk.
1) I wonder if it is possible to visualize the data from propka in PYMOl or another visualization program? I would like to look at how charges are distributed on my model protein (lysozyme, PBD 2XBR).
2) Another thing: Should I manually remove the Heteroatoms (ligand ect.) before I load the pdb-file in propka 3.0?
I am happy to hear you found the talk interesting.
1) Do you want something like coloring positive residues blue, and negative residues red, for a particular pH?
Pymol can display an electrostatic potential map created using APBS. Input for APBS is generated by another program called PDB2PQR, which in turn uses PROPKA.
So that's one (somewhat complicated) option. An easier option is simply to select the residues you want and color them yourself based on the PROPKA results. Let me know if you want more details.
2) PROPKA3.0 ignores heteroatoms, so you don't have to remove them. There are a few exceptions such as some atomic ions, like Ca2+.
2 comments:
Hi Jan
I went to the Ph.D. course two weeks ago - thank you for an interesting talk.
1) I wonder if it is possible to visualize the data from propka in PYMOl or another visualization program? I would like to look at how charges are distributed on my model protein (lysozyme, PBD 2XBR).
2) Another thing: Should I manually remove the Heteroatoms (ligand ect.) before I load the pdb-file in propka 3.0?
Hi Mette,
I am happy to hear you found the talk interesting.
1) Do you want something like coloring positive residues blue, and negative residues red, for a particular pH?
Pymol can display an electrostatic potential map created using APBS. Input for APBS is generated by another program called PDB2PQR, which in turn uses PROPKA.
So that's one (somewhat complicated) option. An easier option is simply to select the residues you want and color them yourself based on the PROPKA results. Let me know if you want more details.
2) PROPKA3.0 ignores heteroatoms, so you don't have to remove them. There are a few exceptions such as some atomic ions, like Ca2+.
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