pyDelPhi-server

About pyDelPhi Webserver

The pyDelPhi Webserver provides a streamlined interface for biomolecular electrostatics calculations using pyDelPhi, a Python-based implementation of the DelPhi Poisson-Boltzmann solver. The current public workflow accepts PQR inputs, which already contain the atomic charge and radius information required for electrostatics calculations.

The server supports standard pyDelPhi calculation options and can generate electrostatic energies and visualization-ready potential or dielectric maps, depending on the selected settings.

PDB-based submission is supported only when compatible charge and size parameters are available. The server does not currently perform pKa prediction, protonation, missing-atom repair, or structure preparation. If results are used in published work, please cite the appropriate DelPhi and pyDelPhi references as described here. Standalone pyDelPhi package is available free of charge for download here.

We acknowledge NIH-Grant# 1R01GM093937 for supporting this work.

Please see the publication for greater details and cite to acknowledge the use of pyDelPhi in work resulting into publication:

Panday, S.K., Zhao, S. and Alexov, E., Accurate and Scalable Continuum Electrostatics for Large Biomolecular Systems: The pyDelPhi Poisson–Boltzmann Framework. Journal of Chemical Information and Modeling 2025 66(1), pp.488-502. https://pubs.acs.org/doi/10.1021/acs.jcim.5c02818

Input Structure

For best results, submit a PQR file. PQR files contain the charge and radius information required for electrostatics calculations. If you only have a PDB file, we will attempt basic structure preparation automatically, but protonation state and charge assignment significantly affect results. We recommend preparing and protonating your structure using the tool appropriate for your system before submitting as PQR.

Upload structure file

Choose PQR or PDB file

PQR is recommended. PDB input is supported using default or custom charge/size files.

Charge/size parameter set

Default CRG/SIZ files are used for standard atoms unless Custom CRG/SIZ is selected.

Custom CRG/SIZ files must be plain text and may contain only letters, numbers, spaces, tabs, newlines, and these symbols: _ - + # ! . E e.

Custom CRG charge file

Choose CRG file

Custom SIZ size/radius file

Choose SIZ file

Poisson-Boltzmann Model

PB formulation

PB approximation

Grid, Solvent, and Dielectric

Gridbox type

Grid scale

Percent fill

Gridbox margin / solute padding Consider 20–30 Å for highly charged or strongly asymmetric systems.

Surface method

Dielectric model

Gaussian sigma

Gaussian exponent

Internal dielectric

External dielectric

Probe radius

Salt concentration

Solver and Convergence

Solver

Boundary condition

Maximum linear iterations

Maximum non-linear iterations

Maximum delta phi

Maximum RMSD

Outputs

Energy terms

Grid energy

Polar solvation energy

Coulombic energy

Map outputs

Output PQR

Potential map

Surface map

Map format

Zeta / surface potential

Zeta distance

A webserver interface to “pyDelPhi: A Modern, High-Performance Poisson–Boltzmann Solver”

Professor Emil Alexov Group