DelPhi Web Server

Delphi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.


References in zbMATH (referenced in 8 articles , 1 standard article )

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  1. Li, Jiao; Ying, Jinyong; Lu, Benzhuo: A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule (2019)
  2. Ying, Jinyong; Xie, Dexuan: A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference (2018)
  3. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  4. Xie, Dexuan; Li, Jiao: A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent (2015)
  5. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  6. Decherchi, Sergio; Colmenares, Jose; Catalano, Chiara Eva; Spagnuolo, Michela; Alexov, Emil; Rocchia, Walter: Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution (2013)
  7. Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil: DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes (2013)
  8. Votapka, Lane W.; Czapla, Luke; Zhenirovskyy, Maxim; Amaro, Rommie E.: DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi (2013)