Further analysis of TK models

danielparton commented 9 years ago

Currently we only analyze sequence identity distributions, RMSD distributions, and final energies from the implicit solvent MD refinement step.

More specific analysis has been included for Src and Abl, but it would be good to add further analysis for the TKs in general.

An obvious addition would be a more rigorous assessment of model quality. Possible ideas:

comparison to reference structures, based on features such as RMSD, phi/psi angles, H-bonds etc.
- there are various pieces of software around which do this kind of thing in the context of homology model refinement. Examples: PROCHECK, DSSP, MolProbity
use the Rosetta heuristic scoring function

jchodera commented 9 years ago

MODELLER provides a model score assessment using DOPE: http://salilab.org/modeller/9v7/manual/node242.html

danielparton commented 9 years ago

Plan is to punt on this for now. May revisit, depending upon reviewers' comments

choderalab / ensembler-manuscripts