Best Method for Calculating Solvent Accessible Surface Area?

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Discussion Overview

The discussion centers around the best computational methods for calculating solvent accessible surface area, particularly in the context of protein folding and protein-ligand docking.

Discussion Character

  • Exploratory, Technical explanation

Main Points Raised

  • One participant inquires about efficient methods for calculating solvent accessible surface area in specific biological phenomena.
  • Another participant mentions Midas and MidasPlus as potential tools, suggesting that the code might still be accessible for review.
  • A subsequent reply questions the current relevance of MidasPlus, noting that it has been replaced by Chimera.
  • There is a request for the location of the code related to Midas and MidasPlus.

Areas of Agreement / Disagreement

Participants do not appear to reach a consensus on the best method, and there are competing views regarding the relevance of MidasPlus versus Chimera.

Contextual Notes

There are references to specific software tools and their historical context, but the discussion does not clarify the current capabilities or limitations of these tools in relation to the inquiry.

hefeweizen
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Hi,

what do you think is the best method to determine/calculate in a
computationally efficient way the solvent accessible surface area in
phenomena like protein folding or protein-ligand docking ?

Thanks
 
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This is not my discipline but I recall reading about Midas and MidasPlus a while ago. I think you can still look at the code and see what is going on.

Here is an overview paper, you might take a look, it has a link to MidasPlus.
http://www.netsci.org/Science/Compchem/feature14e.html
 
do you know where the code can be found ?

jim mcnamara said:
This is not my discipline but I recall reading about Midas and MidasPlus a while ago. I think you can still look at the code and see what is going on.

Here is an overview paper, you might take a look, it has a link to MidasPlus.
http://www.netsci.org/Science/Compchem/feature14e.html
 

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