From: Chih-Ying Lin <chihying.usc.edu>
Date: Sun, 04 Apr 2010 17:39:45 -0700


if i select a group consisting of a single residue, which is in the core of a protein, it is impossible that water penetrates into the core of the protein so SAS is supposed to be zero.

=> However, the SAS_calculation of the single residue residing in the core of the protein is NOT ZERO.

=> My understanding is that SAS returns the surface area of the single residue and it does not matter where the single residue locates.

=> The single residue can locate in the core of the protein or on the surface of the protein. The SAS calculation for the single residue will not make a huge difference unless the single residue deforms/ twists ..... on the surface or in the core of the protein,right ?

=> How to compute protein-protein interface area?

=> In the protein + ligands + water system, I want to compute protein-ligand interface, protein-water interface, and ligand-water interface separately. => How?

=> in the protein + water system, the total SAS fluctuates between 88 and 144 (angstrom_squares)
=> does it make sense ?
=> I don't think that protein will swell 50 % plus in the pure water.
=> But why ??

=> How to calculate the surface area of a micelle ?

Thank you


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Received on Sun Apr 04 2010 - 18:00:02 PDT
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