Quaid-i-Azam University National Center for Bioinformatics A XIAL F - - PowerPoint PPT Presentation

AXIAL FREQUENCY DISTRIBUTION

By Saad Raza Syed Sikander Azam

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Quaid-i-Azam University National Center for Bioinformatics

STEROL 24-C-METHYL TRANSFERASE

 METHOD

 Molecular modeling

and docking of SMT and comparative dynamic studies of docked and undocked protein

 RESULTS

 Discovery of potential

candidate that exhibited improved, interactive binding as compare to the commercially available drug.

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AXIAL FREQUENCY DISTRIBUTION

 Atomic molecular distribution of ligand atoms

against protein atoms relative to the coordinate axis can give the insight into coordination geometry of the enzyme-inhibitor complex and further establish their stability.

 The AFD is calculated on the basis of :

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

l k, j= = i j i,

m = AFD

1 1,

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AFD ALGORITHM DEVELOPMENT

 Initially frequency was calculated from normal

amber mdcrd trajectory file.

 Initially Perl programming language was used to

extract the relative position of the bonding atom

 Currently the code has been impelmented in C++.  Output of the program is a MATLAB readable 3d

histogram file which is later on converted into a 3d histogram using MATLAB.

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INPUT FILES REQUIRED

 For running the AFD algorithm we need the

atom name and residue of the interacting partners.

 Files required  AMBER topology file of the simulation trajectory  Input configuration file listing trajectories and the

atom and residue names

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 Matlab script 

[Z]= reshape(textread(‘filepath','%n'),100,100) [X,Y]=meshgrid(-5:.1:5) Z(Z == 0) = NaN mesh(Z)

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ACKNOWLEDGEMENT

 We would like to acknowledge our lab members.

HEC (Pak) Ernst Mach (Austria) IFS (Sweden)

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QUESTION AND ANSWER

 Any further information can be obtained from the

authors via email.

 Syed Sikander Azam syedazam2008@gmail.com  Saad Raza

saadraza128@gmail.com

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