Related Experiment Video
Updated: Mar 31, 2026
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs
Lin Wang1, Min Zhang2, Emil Alexov1
1Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and.
Unlabelled:
A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol.
Implementation:
The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs.
Availability And Implementation:
The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver.
Related Concept Videos
02:47Protein Families
01:49Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...