Why is it only now or just recently, project t344 casp7 seems to be the only project that is popping up with the low negitive scores?

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Most of the jobs that are currently running are for the refinement category of CASP7 in which structures are provided that are close to the native structure and the challenge is to get even closer for high resolution models. Since we are starting with close to native structures, the energies are low.

For more info about CASP7 goto their web site at: http://predictioncenter.org/casp7.

Most of the jobs that are currently running are for the refinement category of CASP7 in which structures are provided that are close to the native structure and the challenge is to get even closer for high resolution models. Since we are starting with close to native structures, the energies are low.

Just out of couriosity, is there a relation between the number of amino acids and the lowest possible energy? In other words: If I have a protein with X amino acids and a (currrently crunched) lowest energy of Y, can I determine if the energy is good or bad?

Just out of couriosity, is there a relation between the number of amino acids and the lowest possible energy? In other words: If I have a protein with X amino acids and a (currrently crunched) lowest energy of Y, can I determine if the energy is good or bad?

Not necessarily, as there are very different interactions between the amino acids. Interactions between fat-like amino acids are much weaker than those between charged groups or by forming hydrogen bonds. So a large protein with mostly fat-like amino acids may have a comparably high lowest energy while a short one made up of many charged groups and having a lot of hydrogen bonds is lower in energy.

Such drastic cases are however rare and you will mostly see a good lowest energy that is in the range of something between -1.8 times to -2.5 times the number of amino acids.

But that range is too imprecise a measure to judge anything. As you can see in the "Top predictions" you may have very low energies and though the RMSD is high, meaning the structure is very far from the native one (if mostly only by one branch or so that kind of dangles in the wrong direction). On the other side a higher energy can belong to a very good structure where only one side chain is placed so unlucky that it generates a high repelling force, say by two identical charges being brought close together.

Bottom line: can I recognize promising values? Yes. Can I recognize values that are definitely good? No.


Regards,

Christoph

P.S.: the number of amino acids of a protein can be found in the .pdb files in the folder BOINCprojectsboinc.bakerlab.org_rosetta. Look at the starting number in the list:

ATOM 1 N MET 1 0.000 0.000 0.000 1.00 1.00

sometimes it is not "1".


Find the last line of the list (not at the bottom, you need to scroll down):

ATOM 2684 2HB SER 174 14.636 44.403 29.688 1.00 1.00

This sample (t368) has 174 amino acids, it could be between -300 and -400 or maybe -450 for a promising structure. The two I am having right now are -349 and -361.

edited for "spelling" - missing minus

Not necessarily, as there are very different interactions between the amino acids. Interactions between fat-like amino acids are much weaker than those between charged groups or by forming hydrogen bonds. So a large protein with mostly fat-like amino acids may have a comparably high lowest energy while a short one made up of many charged groups and having a lot of hydrogen bonds is lower in energy.
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WOW! Thanks for the detailed answer!

Yes thanks Christoph. That's very helpful :-)