In the first paper, the energy is higher, but the RMSD is lower. In the second paper, the RMSD is higher, but the energy is lower. How did this happen?
Well, in the first paper, phi/psi angles are set directly from a library of sequentially homologous dipeptides to pentapeptides that INCLUDES MELITTIN. So, by the time you get to tripeptides, you're nearly guaranteed to just be outputting the native conformation phi/psi angles over and over again. And this paper is just one of many to make basic mistakes like this.
As young turk back then, I got into a rather long and vigorous online argument with one of the founders of CASP who insisted the first paper was a partial solution to the protein folding problem. And I suspect that argument influenced the subsequent creation of CASP.
Anyway, it's been nice rehashing my post-doc glory days(tm), but we no longer have any excuses here. We have the tools, we have the technology...
Here's an example of what drove my work back then:
Look at the energies and RMSDs (a measure of distance from the native structure) of melittin in these two papers:
Table 2 in http://onlinelibrary.wiley.com/doi/10.1002/pro.5560020508/pd...
and
Table 1 in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1260499/pdf/biop...
In the first paper, the energy is higher, but the RMSD is lower. In the second paper, the RMSD is higher, but the energy is lower. How did this happen?
Well, in the first paper, phi/psi angles are set directly from a library of sequentially homologous dipeptides to pentapeptides that INCLUDES MELITTIN. So, by the time you get to tripeptides, you're nearly guaranteed to just be outputting the native conformation phi/psi angles over and over again. And this paper is just one of many to make basic mistakes like this.
As young turk back then, I got into a rather long and vigorous online argument with one of the founders of CASP who insisted the first paper was a partial solution to the protein folding problem. And I suspect that argument influenced the subsequent creation of CASP.
Anyway, it's been nice rehashing my post-doc glory days(tm), but we no longer have any excuses here. We have the tools, we have the technology...