ADL: protein preparation..

Savani Anbalagan savani1987 at gmail.com
Tue Oct 9 07:29:37 PDT 2007


Hi autodockers..



in the protein preparation step do we need to energy minimize the protein
structure?

because in tis paper http://dx.doi.org/10.1016/j.bmcl.2005.07.043     check
out 2.2. 1GOS (3.0 Å resolution)

it goes like this..

For use with the Autodock docking simulation, all polar hydrogens were added
with the GROMACS modeling
package.18<http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF9-4H0J8H5-4&_user=3068220&_coverDate=10%2F15%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059620&_version=1&_urlVersion=0&_userid=3068220&md5=864df73c0fd2cc59610f8667bc143c43#bib18>and
19<http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF9-4H0J8H5-4&_user=3068220&_coverDate=10%2F15%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059620&_version=1&_urlVersion=0&_userid=3068220&md5=864df73c0fd2cc59610f8667bc143c43#bib19>The
partial charges were placed using the same package keeping FAD in an
oxidized sate. The resulting structure was optimized in 400 steps of
conjugate gradient minimization, employing the GROMACS87 force field. During
minimization, the heavy atoms were kept fixed at their initial crystal
coordinates, but added hydrogens were made free to move. Minimization was
effected under a vacuum medium. Electrostatic interactions were calculated
using the cut-off method. As the acceptable minimal force gradient was
reached, the minimization converged and the resultant structure was saved.
Finally, solvation parameters were added using the ADDSOL utility of
AutoDock 3.0.5. Default values of atomic solvation parameters were used
throughout the calculations. The grid maps of the protein used in the
docking experiments were calculated using the AutoGrid utility program.


when is this necessary???

this author has tried to extract protein from a protein ligand complex is
that's the reason why he has gone for energy minimization???


say if i dont have the protein-ligand complex and i have the structure of
protein alone, do i have to energy minimize the protein structure before i
docking?



Thanx in advance..


With Regards,


Savani Anbalagan
Masters Industrial Biotechnology
SASTRA University,
India


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