The required file of Evaluation_qmeandisco method

[wt12318]

Hi,

I am confused about the three files required by Evaluation_qmeandisco(https://homelette.readthedocs.io/en/latest/evaluation.html#homelette.evaluation.Evaluation_qmeandisco):

Requires the following valid entries in the model.info dictionary:

- accpro_file (.acc file)
- psipred_file (.horiz file)
- disco_file (generated by qmean.DisCoContainer.Save)

How to generated these files? Thank you.

Tao Wu

[PhilippJunk]

Hi,

generating the files necessary to run Evaluation_qmeandisco is indeed a bit confusing, sorry if the documentation is not detailed enough on this.

For the full QMEANDisCo prediction, you need

• Solvent accessibility predictions generated with ACCPro.
• Secondary structure predictions generated with PSIPRED.
• Distance constraints of related structures created with the qmean python package.

All of these need to be only run once for a target sequence, which is why they were not included in the Evaluation method itself (which would re-run it for each generated model).

ACCPro can be downloaded from here, there should also be some documentation for it.

PSIPRED can be downloaded from here.

QMEAN is already installed in the docker container. However, there is no online documentation, you have to build it yourself. Instructions along with the source are here. In the documentation, there is an explanation how to generate and save the disco_file.

For ACCPro and PSIPRED, I am pretty sure that there are web servers available to generate the necessary files. If you only have a few target structures, it might be easier to use those as setting up these programs was a bit tedious if I remember correctly.

Hope this was helpful, Philipp