DelPhiPKa Webserver

About DelPhiPKa Web Server

DelPhi-PKA is a DelPhi-based C++ program, allowing pKa prediction for ionizable groups in proteins, RNA and DNA.

Unique approach stems from:
a) Use gaussian-based smooth function to mimic conformational changes associated with ionization changes.
b) Calculate the electrostatic energy without defining molecular surface.

For questions and help, please contact the project support channel.

Source code and installation files are available on the DelPhiPKa GitHub Page. User Manual can be found through the documentation links on this site.

If the use of DelPhiPKa results in a publication, please cite the appropriate references and user manual.

Dear Users. Please, do not submit many jobs (especially jobs with large PDB files), because this requires significant computation and affects the work of our users. Instead, download the stand-alone version of DelPhiPKa and run it on your computer. Thank you for understanding.

Please do not submit files with more than 60 titratable residues since their computation exceeds the wall time of the cluster. Instead download and install DelPhiPKa on your computer.

Input Structure

PDB/PQR is the primary upload type. PDB/PQR inputs are processed with the selected force-field charge and size parameters. PQR content may include HETATM records encoded in PQR-like format when the appropriate options are selected.

Upload PDB/PQR file

Choose PDB or PQR file

Use Amber, CHARMM22, or PARSE for PDB input.

Force field

DelPhiPKa Options

Calculate more titratable residues

Remove HETATM

Remove water molecule

HETATM in PQR format

Output PQR with pKa result

Hydrogen of ASP attached atom

Hydrogen of GLU attached atom

Variance of Gaussian distribution

Salt concentration

Reference dielectric

External dielectric

Given pH value

pH initial value

pH end value

pH interval

DelPhiPKa: A protonation and pKa calculation web server

Professor Emil Alexov Group