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Journal Club Presentation Brett Zirkle 2/8/2012

DelPhi Web Server v2: Incorporating atomic-style geometrical figures into the computational protocol Alexov Group Clemson University Submitted to Structural Bioinformatics. Journal Club Presentation Brett Zirkle 2/8/2012. Highlights. Nano -objects. Accessibility. How it works….

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Journal Club Presentation Brett Zirkle 2/8/2012

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  1. DelPhi Web Server v2: Incorporating atomic-style geometrical figures into the computational protocol Alexov Group Clemson University Submitted to Structural Bioinformatics Journal Club Presentation Brett Zirkle 2/8/2012

  2. Highlights Nano-objects Accessibility

  3. How it works… Load PDB File and Input Parameters Specify Desired Output

  4. Nano-objects: How it works… Set coordinate parameters

  5. Results/Output Files Output files: amino acid charge (.crg), atomic radius (.siz), protonated PDB file, potential phimap in cube format (.cube)

  6. Poisson-Boltzmann Solvers Delphi Adaptive PB Solver [ε(r)Φ(r)] – ε(r)[8πq2I/εkBT]sinh [Φ(r)] + 4πρf(r)/kBT = 0 Electrostatic potential Ionic strength Charge density Dielectric constant Boltzman constant

  7. Poisson-Boltzmann Solvers q2 [ε(r)Φ(r)] – ε(r)[8πq2I/εkBT]sinh [Φ(r)] + 4πρf(r)/kBT = 0 Electrostatic potential Ionic strength Charge density Dielectric constant Boltzman constant

  8. How APBS works… Generate PQR File: Load PDB into server and input parameters Output: Protonated PDB file with atomic radii and charges Pymol: Load PQR in APBS solver

  9. Qualitative Comparison of Electrostatic Maps Delphi Adaptive PB Solver 3QSV

  10. Qualitative Comparison of Electrostatic Maps Delphi Adaptive PB Solver 2A0I

  11. Qualitative Comparison of Electrostatic Maps Delphi Adaptive PB Solver 3GPL (ssDNA)

  12. Summary and Final Thoughts • Delphi web server • Quick (25min) and easy way to generate Delphi potential map • Easy to use interface • Can visualize using Jmol in browser • Insert nano-objects and carry out electrostatic calculations in the presence of biological macromolecules • Paper suggestions • Include examples as an additional figure • Information about the server performance may be useful • All in all… • The Delphi web server provides a simple and easy to use tool for visualizing electrostatic potentials

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