DelPhiPKa Web Server

Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

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All the jobs in queue are deleted. Due to maintenance of Palmetto supercomputer. If you are still interested please resubit your job.

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.

DelPhiPKa protonation and pKa calculation web server

Delphi-PKA is a DelPhi-based C++ program, allowing to predict pKa's 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, email to delphi@g.clemson.edu

Source code and installation files are on DelPhiPKa Github Page. User Manual can be found here.

If the use of DelPhiPKa results to a publication, please cite these references.

Click on the following links to obtain a sample PDB file along with a table with predicted results. This is for training purposes.

Upload PDB File: Please ensure that the file size doesn't exceed 20MB.

Force Field:

Calculate more titratable residues (Ser, Tyr, Thr, Cys): Enable this will dramatically increase the running time

Remove HETATM:

Remove Water Molecule:

HETATM in PQR format:

Output PQR File 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:

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