I'm trying to compute and represent the electrostatic potential (Poisson-Boltzmann) of some proteins to verify if they can potentially bind in their complementary interfaces. Is there any bioinformatic software to do this in an easy way?
Hi Claudia,
To calculate a protein's Poisson-Boltzmann potential, I recommend you using PDB2PQR and APBS. You can run both on their web server, and you just need a .pdb file (or just a PDB ID) to run them. PDB2PQR gets a .pdb file as input, and gives you a .pqr file, which contains electrostatic field coordinates, and an .in file, which is the input for APBS. APBS computes the Poisson-Boltzmann potential, and gives you a .dx file as an output. You can find more info about running both programs in this link: http://www.poissonboltzmann.org/docs/home/
To represent the electrostatic potential you have already calculated, you can load the .dx file over a protein surface, created with any molecular visualization program, such as Chimera or PyMol.
It's been a while since last time I did it, so I may be mistaken, or I may have forgotten some points. If you have any question, or you find something unclear, please notice me.
Hope this helps you.
http://www.poissonboltzmann.org/docs/home/
Muchas gracias Juan, fue de mucha utilidad y finalmente ya pude calcular los EPs usando PDB2PQR y visualizarlos usando Chimera. Te agradezco mucho la ayuda!!!
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