DelPhi (software)

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DelPhi

The electrostatic field lines of TRAP---trp RNA binding attenuation protein (PDB ID: 2EXS). The blue and red colors represent the positive and negative polarities, respectively. The field lines indicate the directions of the electrostatic forces surrounding the protein.
Original author(s) Barry Honig
Developer(s) DelPhi Development Team
Operating system Linux, Mac OS X, Microsoft Windows
Website http://compbio.clemson.edu/delphi.php

DelPhi is a scientific application which calculates electrostatic potentials in and around macromolecules and the corresponding electrostatic 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. [1] [2] [3]

Pdb files are typically used as input for DelPhi calculations. Other required inputs are an atomic radii file and a charge file .[4] 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.[5]

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.[6]

See Also

External links

References

  1. ↑ "Software:DelPhi". Honig Lab. Columbia University. 
  2. ↑ Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (January 2002). "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". J Comput Chem 23 (1): 128–37. doi:10.1002/jcc.1161. PMID 11913378. 
  3. ↑ Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E. (May 2012). "DelPhi: a comprehensive suite for DelPhi software and associated resources.". BMC Biophysics 5. doi:10.1186/2046-1682-5-9. PMID 22583952. 
  4. ↑ "DelPhi Parameter Files". 
  5. ↑ DelPhi manual
  6. ↑ Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B (October 2009). "The role of DNA shape in protein-DNA recognition". Nature 461 (7268): 1248–53. doi:10.1038/nature08473. PMC 2793086. PMID 19865164. 


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