Introduction

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.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.The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver.

Publications

  1. DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.
    Cite this
    Wang L, Zhang M, Alexov E, 2016-02-01 - Bioinformatics (Oxford, England)
  2. pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
    Cite this
    Wang L, Li L, Alexov E, 2015-12-01 - Proteins

Credits

  1. Lin Wang
    Developer

    Computational Biophysics and Bioinformatics, Department of Physics and Astronomy

  2. Min Zhang
    Developer

    Department of Computer Sciences, East Carolina University, United States of America

  3. Emil Alexov
    Investigator

    Computational Biophysics and Bioinformatics, Department of Physics and Astronomy

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Summary
AccessionBT001701
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByEmil Alexov