Delphi Workshop
Content Inside: Delphi is a powerful computational tool developed by Barry Honig and his research group at Columbia University. Delphi is a solver of the Poisson-Boltzmann (PB) Equation. 1-3 The PB equation is used in implicit solvation calculations. Implicit solvation techniques are used to account for the effects of a solvent (e.g. water) without having actual solvent (water) molecules included in the model. 2 0 int ( ) ( ) ( ) 4 ( ) 0 r r r r + = The linearized PB equation. = vector differential operator (/x) + (/y) + (/z) (r) = dielectric function (r) = electrostatic potential = Debye-Hckel inverse length. int (r) = interior charge density A three dimensional grid of defined density surrounds the system in a cubic box. Each grid point represents a dielectric constant (either in solvent (water) or in solute (protein interior)). Either the molecular surface or solvent accessible surface is used to determine the boundary between the solute and the solvent. Typically, the solvent accessible surface is used. NOTE: Delphi reports energy in units of kT. (1 kT = 0.592 kcal/mol for T = 298 K and k = 0.001986577 kcal/molK) Make a separate project directory (e.g. del_tutor). You will study the binding in the barstar/barnase complex. We will use PDB entry 1BRS for this study. 4 This complex has been investigated extensively using Delphi and is a good instructional example. 5, 6 Download 1BRS.PDB from the Protein Data Bank ( http://rutgers.rcsb.org/pdb/ ). 3 This structure has missing side chains and residues. We used the profix program in the JACKAL molecular modeling package 7 to replace missing residues and missing sidechains. JACKAL is not yet available on UMDNJ servers/workstations other than linux boxes; however, it is freely available for unix/linux platforms at http://trantor.bioc.columbia.edu/programs/jackal/ . The fixed pdb file ...
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