DelPhi Web Server swMATH ID: 17209 Software Authors: Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia, Emil Alexov Description: 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. Homepage: https://www.cambridge.org/core/journals/communications-in-computational-physics/article/delphi-web-server-a-comprehensive-online-suite-for-electrostatic-calculations-of-biological-macromolecules-and-t Related Software: MIBPB; FEniCS; PDB2PQR; APBS; SDPBS; PBEQ-Solver; CHARMM; SyFi; DOLFIN; PETSc; VMD; tabipb; TABI; AFMPB; SMPBS; Python; Jmol; SIB-BLAST; PUDGE; FoldX Cited in: 8 Documents Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Zbl 1373.92003Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil 2013 all top 5 Cited by 20 Authors 4 Xie, Dexuan 3 Ying, Jinyong 2 Alexov, Emil 2 Li, Jiao 2 Rocchia, Walter 2 Zhenirovskyy, Maxim 1 Amaro, Rommie E. 1 Catalano, Chiara Eva 1 Colmenares, Jose 1 Czapla, Luke 1 Decherchi, Sergio 1 Jiang, Yi 1 Lu, Benzhuo 1 Sarkar, Subhra 1 Spagnuolo, Michela 1 Votapka, Lane W. 1 Witham, Shawn 1 Xie, Yang 1 Yu, Zeyun 1 Zhang, Jie Cited in 5 Serials 3 Communications in Computational Physics 2 Journal of Computational Physics 1 Applied Mathematical Modelling 1 Nonlinear Analysis. Real World Applications 1 Molecular Based Mathematical Biology Cited in 5 Fields 6 Biology and other natural sciences (92-XX) 3 Optics, electromagnetic theory (78-XX) 2 Numerical analysis (65-XX) 2 Computer science (68-XX) 1 Partial differential equations (35-XX) Citations by Year