Final Presentation - December 13, 2002
By Parag Jain
- Goal: The goal of this project is to compare algorithms for computing molecular surfaces and to make an inference as to what the best algorithm for such computation is.
- Molecular Surface: A molecular surface (MS) is defined by Lee and Richards (1971 ref.) as the surface resulting from rolling a probe sphere on the van der Waals surface.
- Types of surfaces:
- Solvent-excluded surface that is traced by the portion of the probe sphere surface facing the van der Waals surface.
- Solvent-accessible surface that is traced by the center of the probe sphere.
- Our Project: For our project we are computing and comparing the Solvent-excluded surfaces (SES) obtained by various algorithms. SES consists of three parts: contact surface, toroidal surface and reentrant surface.
- The contact surface is made up of "those parts of the molecular van der Waals surface that can actually be in contact with the surface of the probe."
- The toroidal surface or the saddle-shaped surafce is made up of "those surfaces where the probe atom is in contact with two atoms."
- The reentrant surface or the concave bowl-shaped surface is made up of "those surfaces where the probe is in contact with three atoms."
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