HI
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.
right?
=> 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
Lin
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Received on Sun Apr 04 2010 - 18:00:02 PDT
