Chandrajit Bajaj

Protein Protein Interaction

 Introduction | Representation | Function | Dynamic structure | Hierarchical model | Protein docking | Simulations | Meshing | Visualization

3. Functional representations

Apart from just the shapes, we are also interested in volumetric functions, whose contours define a better estimate of shape, and can be used for animation, docking and other calculations. Some important fields we are interested in are electron density and electrostatic potential. 

We have developed an electron density field estimation program which inputs either PDB or PQR data and calculates a function of electron density. Gaussian kernels are approximated around each atom, the magnitude and extent being determined by the atom type. APBS, a package from Nathan Baker is used to obtain the electrostatic potential calculation. One of the functions used to evaluate this field is the sum of bonded and non bonded energies, calculated from summing up the contributions of all atoms and their bond energies.

  • Electrostatic density evaluation package which uses a Gaussian kernel to approximate the field
    Electron density Laplacian of electron density Electrostatic gradient magnitude

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