Final Presentation - December 13, 2002
By Parag Jain
My efforts towards the Project
- Delaunay Triangulations calculation using "divide-and-conquer" algorithm:
- The divide-and-conquer algorithm subdivides the area into two partial areas, computes recursively the Delaunay triangulation of the partial areas and merges finally both triangulations.
- Molecular Surface computation using "Distributed Molecular Surface" (DMS):
- DMS computes the molecular surface (SES) of a molecule.
- Author: Conrad Huang, 2002.
- Used DMS to conduct several runs for a set of sixteen molecules.
- Worked with DMS with one of my colleagues until I got the source code for another algorithm (MASKER) that did the same.
- Molecular Surface computation using "Improved solvent excluded molecular surface area estimations using Boolean masks" (MASKER):
- Masker computes the SES for a molecule.
- This algorithm is based on the boolean mask approach that was proposed by LeGrand and Merz (Le Grand and Merz 1993). This algorithm takes the method of Le Grand and Merz one step further by using masks to calculate SES.
- Author: Christopher Bystroff, 2001.
- As of today I have used MASKER to conduct test runs for around 95 molecules including proteins, DNAs, and RNAs.
- The plot of the times that MASKER took to compute the molecular surface versus the number of atoms in the molecule fits best with the graph of polynomial with an exponent of approximately 1.64 (for proteins), 1.13 (for DNAs), 1.22 (for RNAs).
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