Best Method for Calculating Solvent Accessible Surface Area?

In summary, there is a tool called MidasPlus that can be used to determine the solvent accessible surface area in phenomena like protein folding or protein-ligand docking. However, it has been replaced by a newer tool called chimera. The code for MidasPlus can still be found online and there is an overview paper available with a link to the tool.
  • #1
hefeweizen
5
0
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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  • #2
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
 
  • #3
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
 

FAQ: Best Method for Calculating Solvent Accessible Surface Area?

What is solvent accessible surface area (SASA)?

Solvent accessible surface area (SASA) is a measure of the surface area of a molecule that is accessible to a solvent, such as water. It is an important parameter in the study of protein structure, as it can provide insight into the shape, size, and hydrophobicity of a protein.

How is SASA calculated?

SASA is typically calculated using a mathematical algorithm that takes into account the size and shape of the molecule, as well as the properties of the solvent. The most commonly used method is the Shrake-Rupley algorithm, which divides the molecule into small spheres and calculates the surface area of each sphere that is accessible to the solvent.

Why is SASA important in protein structure prediction?

SASA is important in protein structure prediction because it can provide valuable information about the folding and stability of a protein. Proteins with larger SASA tend to be more flexible and have a higher likelihood of being unstructured, while proteins with smaller SASA are more likely to be well-folded and stable.

How does SASA relate to protein-protein interactions?

SASA plays a crucial role in protein-protein interactions. Proteins with complementary SASA can interact more easily, as their surfaces can fit together like puzzle pieces. On the other hand, proteins with very different SASA may not interact as effectively, as their surfaces may not be able to form strong interactions.

Can SASA be used to predict the binding affinity between two proteins?

While SASA can provide important information about the surface complementarity between two proteins, it is not the sole factor in determining binding affinity. Other factors, such as the strength of individual interactions and the presence of other molecules, also play a role in protein-protein binding. However, SASA can be a useful tool in predicting the likelihood of two proteins interacting with each other.

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