title: DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.
abstract: 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.
  
  
  METHODS
  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.
  
  
  METHODS
  The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver.
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and.
authors.forename: Lin
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Computer Sciences, East Carolina University, Greenville, NC 27858, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and.
authors.forename: Emil
authors.initials: E
authors.lastname: Alexov
mesh_terms: D004247:DNA / Q000737:chemistry*; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012984:Software; D055672:Static Electricity
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA