I see. I just asked because there was no explanation about your method avilable.
Ok, I can also add that in your cause, it is not so difficult to reproduce this "spontaneity" as your ligand contains phosphate groups and therefore high negative charge and on the binding pocket it seems to be a predominancy of positively charged residues like ARG and similar ones. Anyway congratulations. I guess, if the ligand did not contain phospahtes, it woule be more difficult to get it to the binding pocket
You may find more about the method, and a link to a related journal paper, by clicking the down arrow right of the text description (to show more information) - there is a link to a web page there that will be informative.
There is no scoring function---these are MD simulations, which use physics-based potential energy functions (a 'force field') to describe interactions between pairs of atoms. The movements shown in the video is from integration of Newton's equations of motion for all the atoms in the system. This is in contrast to more empirical approaches such as docking, which uses a semi-physics-based scoring function to predict the final binding pose of a ligand directly.
I see. I just asked because there was no explanation about your method avilable.
Ok, I can also add that in your cause, it is not so difficult to reproduce this "spontaneity" as your ligand contains phosphate groups and therefore high negative charge and on the binding pocket it seems to be a predominancy of positively charged residues like ARG and similar ones. Anyway congratulations. I guess, if the ligand did not contain phospahtes, it woule be more difficult to get it to the binding pocket
Yeclanoide 1 year ago
@Yeclanoide
You may find more about the method, and a link to a related journal paper, by clicking the down arrow right of the text description (to show more information) - there is a link to a web page there that will be informative.
tcbguiuc 1 year ago
which scoring function are you using?
Yeclanoide 1 year ago
@Yeclanoide
There is no scoring function---these are MD simulations, which use physics-based potential energy functions (a 'force field') to describe interactions between pairs of atoms. The movements shown in the video is from integration of Newton's equations of motion for all the atoms in the system. This is in contrast to more empirical approaches such as docking, which uses a semi-physics-based scoring function to predict the final binding pose of a ligand directly.
tcbguiuc 1 year ago
Very cool. I look forward to some videos involving ATP. The time scale of only one microsecond really requires a mental adjustment.
I assume the simulation involves the surrounding water molecules (not shown) as well?
Ironstead 3 years ago
Yes, the water molecules are explicitly included in the simulation, but not shown in the movie.
tcbguiuc 3 years ago