Welcome to Ape-Gen 2.0!

Peptide*

Peptide Input (see help for specification?)

MHC Allotype*

MHC allotype input

Step 2: Anchor Definition and Tolerance

Anchor Selection*

Calculate anchors automatically Speficy anchors

Either automatic or manual selection of anchors

Anchors*

Define the anchors manually (must be integers separated by commas)

Anchor priority*

Primary/Secondary Primary None

Select the anchor category that you want to apply anchor tolerance on.

Anchor Tolerance*

Define anchor tolerance in relation to the peptide template

Step 3: Backbone generation parameters:

RCD Step*

Default values Custom values

#Loops Generated*

#Loops to be Scored/Optimized*

Tol.*

Sampling ratio*

Loop Score Selection*

Loop ranking score selection

CAUTION!!: Expect Ape-Gen runtime to increase as RCD arguments change

Step 4: Scoring/Optimization parameters:

Scoring Function*

Vinardo Vina

Scoring function selection

Flexibility*

Rigid Receptor Flexible Receptor

Select the state of receptor during docking/optimization

Energy Minimization

Select this box if you would like to further optimize the ensemble with an energy minimization step using openMM.

Step 6: Don't forget your e-mail!

User email*

Your email address will only be used to send you a link to the pMHC modelling results

How to cite Ape-gen

If you publish results obtained using APE-Gen2.0, please check how to cite our work.

Disclaimer

Due to the web server's nature, functionality is limited to specific arguments, spfici MHC alleles etc. If you want to use the full functionality of APE-Gen2.0, it is best to visit the github page and either install it locally, or use the docker image provided. Visit the github link for more info (will be provided in the future)

Privacy policy

Data and results of each user are not accessible to other users, but we cannot guarantee full privacy. We assume the data submitted to APE-Gen2.0 is not strictly confidential.

Data retention policy

Data and results will be periodically deleted at the start of each month. If you want to store structures that you are producing with APE-Gen2.0, please use the download feature in the results tab.