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^ Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E (2012).

'Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects'.

^ Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002).

Journal of Chemical Theory and Computation. 'On the Dielectric 'Constant' of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi'.

^ Li L, Li C, Zhang Z, Alexov E (2013).

'The role of DNA shape in protein-DNA recognition'.

^ Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B (October 2009).

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For example, the elapsed time in the PC version is not calculated at present.Įach distribution contains one executable (named delphi or delphi.exe), the source codes (with corresponding makefile when needed), and some worked examples.

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Their way of working is very similar however, unexpected differences may appear due to different numerical precision or to the porting of the software to different architectures.

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PC version, compiled under Windows Operating System, using Microsoft Developer Studio C++ and Fortran compilers.

LINUX version, compiled under Red Hat 7.1, kernel 2.4.2 Operating System, using GNU gfortran compilers,.

IRIX version, compiled under IRIX 6.5 Operating System, 64bits, using f77 and cc compilers.

IRIX version, compiled under IRIX 6.5 Operating System, 32bits, using f77 and cc compilers.

ĭelPhi v.7 is distributed in four versions: DELPHI has also been utilized to build a server that predicts pKa's of biological macromolecules such as proteins, RNAs and DNAs which can be accessed via web. DELPHI is also implemented into an accessible web-server.

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Versions ĭelphi distribution comes as a sequential as well as parallelized codes, runs on Linux, Mac OS X and Microsoft Windows systems and the source code is available in Fortran 95 and C++ programming languages. Binary Potential files as output from DelPhi can be viewed in most molecular viewers such as UCSF Chimera, Jmol, and VMD, and can either be mapped onto surfaces or visualized at a fixed cutoff. Other required inputs are an atomic radii file and a charge file. Pdb files are typically used as input for DelPhi calculations. In addition to the typical potential map, DelPhi can generate and output the calculated distribution of either the dielectric constant or ion concentration, providing the biomedical community with extra tools for their research. Features Īdditional features such as assigning different dielectric constants to different regions of space, smooth Gaussian-based dielectric distribution function, modeling geometric objects and charge distributions, and treating systems containing mixed salt solutions also attracted many researchers. The widespread popularity of DelPhi is due to its speed, accuracy (calculation of the electrostatic free energy is only slightly dependent on the resolution of the grid) and the ability to handle extremely high grid dimensions. DelPhi, developed in Professor Barry Honig's lab in 1986, was the first PBE solver used by many researchers. Analytical solutions of the corresponding Poisson-Boltzmann Equation (PBE) are not available for such cases and the distribution of the potential can be found only numerically.

One of the main problems in modeling the electrostatic potential of biological macromolecules is that they exist in water at a given ionic strength and that they have an irregular shape. DelPhi is commonly used in protein science to visualize variations in electrostatics along a protein or other macromolecular surface and to calculate the electrostatic components of various energies. It incorporates the effects of ionic strength mediated screening by evaluating the Poisson-Boltzmann equation at a finite number of points within a three-dimensional grid box.

The field lines indicate the directions of the electrostatic forces surrounding the protein.ĭelPhi is a scientific application which calculates electrostatic potentials in and around macromolecules and the corresponding electrostatic energies. The blue and red colors represent the positive and negative polarities, respectively. The electrostatic field lines of TRAP-trp RNA binding attenuation protein (PDB ID: 2EXS).