CASP Model Analysis :: The “BACPAC” Modules
BACPAC -- Beyond Alpha Carbon Protein Assessment for CASP
In a very distant time-space discontinuum, far removed from here, we did a thing called CASP8. As is our usual approach to our unusual viewpoints of our work-a-day world, we asked ourselves: "Well, guys, what could we maybe do to make all this fun AND add something maybe not done before to this effort called CASP" (more specifically the template-based modeling assessment portion {but that last parenthetical part wasn't part of our question, so it's not in the quotes}). Well, we thought a bit, hum-hawed more, one of us went to Romania for a long time, and we eventually created six mostly new, somewhat borrowed, and all blue metrics which we used in our assessment. The details of which are in
As promised, the methods (software) for calculating these six metrics are presented here for any other visitors to any other space-time discontinuums to use at their own risk and enjoyment. Along with BACPAC (i.e. the software), you may need a travel guide (i.e. documentation) for the six metrics:
- Preprocessor - prepares PDB files for use by BACPAC modules
- MolProbity score
- Mainchain reality score
- Hydrogen bond correctness for mainchain
- Hydrogen bond correctness for sidechain
- Rotamer correctness
- Sidechain positioning
Click ==> 
bacpac.1.04.100802.linux.zip <== to get the heavily discounted package of all modules (real backpack not included)
If you have any questions or suggestions for BACPAC, please email to daniel (dot) keedy (AT) duke (DOT) edu.