Frequently Asked Questions
This page summarizes practical input, output, and citation guidance for the DelPhiPKa web server.
For best results, start with a carefully prepared biomolecular structure with correct atom naming, missing atoms
resolved, and appropriate charge and radius information. PQR input is recommended because it already contains
the partial atomic charges and atomic radii needed for electrostatic pKa calculations.
Question: What is DelPhiPKa?
Answer:
DelPhiPKa is a DelPhi-based tool for predicting pKa values of ionizable groups in biomolecular structures.
Starting from the submitted structure and electrostatic model settings, it estimates pKa shifts and titration
behavior of ionizable groups. Depending on the selected outputs, it can generate pKa tables, titration data,
energy terms, and protonated structures.
Question: What can the DelPhiPKa web server do?
Answer:
The web server lets users submit DelPhiPKa prediction jobs without installing the standalone software.
Users provide a molecular structure and select calculation/output options through the web form. The server
validates the input, generates the runtime parameter file internally, runs DelPhiPKa, and returns selected
result files for download or inspection.
Question: What is a .pqr file?
Answer:
A
.pqr file is an ASCII text structure file that contains atomic position coordinates,
partial atomic charges, and atomic radii. In simple terms, the name reflects:
- P: atomic position coordinates
- Q: partial atomic charge
- R: atomic radius or size
DelPhiPKa requires this charge and radius information to solve the electrostatic problem. A coordinate-only
structure is usually not sufficient unless charges and radii are assigned by the server or by your own
preprocessing workflow.
Question: Which structure format should I upload?
Answer:
PQR input is recommended because it explicitly includes coordinates, charges, and radii. PDB input is allowed,
but the server must be able to assign or locate suitable charge and size parameters. PDB files generally contain
coordinates only, so they may require a compatible force-field selection and appropriate CRG/SIZ parameter data.
Question: Does the server repair or prepare my PDB structure automatically?
Answer:
No. The server does not currently perform pKa-aware structure preparation, missing-atom repair, ligand cleanup,
protonation-state assignment, or molecular modeling before the DelPhiPKa run. Users should prepare structures
carefully before submission and verify that the selected charge and radius parameters are appropriate.
Question: When do I need custom CRG and SIZ files?
Answer:
Custom CRG and SIZ files are needed when you choose a custom parameter workflow for a PDB input. The CRG file
provides atomic partial charges, and the SIZ file provides atomic radii. Standard force-field choices should use
server-managed default charge and size parameters, while custom choices should be accompanied by matching CRG
and SIZ files.
Question: Can I upload my own DelPhiPKa runtime parameter file?
Answer:
No. Runtime parameter files are generated by the server from validated form fields. This keeps the submission
workflow consistent, easier to validate, and safer for the web environment. Users should select options through
the form instead of uploading a prewritten DelPhiPKa parameter file.
Question: Are ions, ligands, or HETATM records supported?
Answer:
They can be included only when the structure and parameter files provide the needed charge and radius information.
Missing or inconsistent parameters can make the calculation unreliable. For nonstandard residues, cofactors,
ligands, or ions, users should verify that the relevant atoms are represented correctly in the input and in any
custom CRG/SIZ files.
Question: What output files can DelPhiPKa produce?
Answer:
Common output files include predicted pKa tables, titration-curve data, energy-term reports, pairwise interaction
reports, and protonated PQR structures. The exact files returned depend on the output options selected during
job submission.
Question: What does pKa.csv contain?
Answer:
The pKa.csv file reports predicted pKa values for ionizable residues. It may also include associated
electrostatic or energy-related terms, depending on the selected calculation and output settings.
Question: What does titra.csv contain?
Answer:
The titra.csv file contains titration-curve data. It describes how the predicted ionization state of
each titratable group changes over the sampled pH range.
Question: How should I visualize DelPhiPKa results?
Answer:
Download the generated structure files and open them in a molecular viewer that supports PDB or PQR files.
Titration and pKa CSV files can be inspected in a spreadsheet program or plotted with your preferred analysis
workflow. Always compare predicted protonation states with the biological context and the quality of the input
structure.
Question: Which references should I cite when using DelPhiPKa results?
Answer:
The following references should be cited if the use of DelPhiPKa results leads to a publication.
In particular, the first reference describes the methodology and the second reference describes the web server.
References:
Lin Wang, Lin Li, and Emil Alexov. "pKa predictions for proteins, RNAs and DNAs with the Gaussian dielectric function using DelPhiPKa." Proteins. (2015) Sep 26, doi: 10.1002/prot.24935
Lin Wang, Min Zhang, and Emil Alexov. "DelPhiPKa Web Server: Predicting pKa of proteins, RNAs and DNAs." Bioinformatics. (2015) Oct 29, doi: 10.1093/bioinformatics/btv607
Swagata Pahari, Lexuan Sun, Sankar Basu and Emil Alexov. "DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate." Proteins. (2018) Sep 25, doi: 10.1002/prot.25608