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hpb description in the main ProDy README
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karolamik13 committed Oct 9, 2023
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Expand Up @@ -72,3 +72,15 @@ with ProDy. The original CE method was developed by Ilya Shindyalov and Philip
Bourne. The Python version which is used by ProDy is developed by Jason Vertrees
and available under the New BSD license.

Hbp module: The calculation of hydrophobic interactions, solvent accessible surface
area (SASA) and volume for each residue is using geometric methods based on the
information of the atoms in the molecule. The methods have been programmed in C++
and can be compiled as a python module “hpb.so” which is then used by ProDy.
Files for compilation are localized at ~/prody/proteins/hpbmodule folder and
required C++ and Fortran compiler. After compilation hpb.so file can be
storage in ~/prody/proteins folder in ProDy or in the local directory which
is used to perform calulations.
C++ code was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel,
Bihua Yu, and Evangelos A. Coutsias (License in ~/prody/proteins/hpbmodule
folder). Details of the method can be found in the Supplementary Material of
InSty manuscript (soon will be submited for publication).

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