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

Quaid-i-Azam University National Center for Bioinformatics A XIAL F REQUENCY D ISTRIBUTION By Saad Raza Syed Sikander Azam 1

S TEROL 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. 2

3

A XIAL F REQUENCY D ISTRIBUTION  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 : k, l  AFD = m i, j i = 1, j= 1 4

5

AFD A LGORITHM 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. 6

I NPUT F ILES R EQUIRED  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 7

8

9

 Matlab script  [Z]= reshape(textread (‘ filepath','%n'),100,100) [X,Y]=meshgrid(-5:.1:5) Z(Z == 0) = NaN mesh(Z) 10

11

ACKNOWLEDGEMENT  We would like to acknowledge our lab members. HEC (Pak) Ernst Mach (Austria) IFS (Sweden) 12

Q UESTION AND A NSWER  Any further information can be obtained from the authors via email.  Syed Sikander Azam syedazam2008@gmail.com  Saad Raza saadraza128@gmail.com 13