I am a new member of the Meiler Lab and for my master thesis I worked with Samuel Schmitz on using co-evolutionary information for protein design, derived from a multiple sequence alignment of homologous sequences with GREMLIN, to favor sequences which recapitulate correlated mutations as observed in nature. We also just submitted our paper (🎉), hoping that you can soon read about the results in detail.
We used a slightly modified version of GREMLIN to generate the tensor storing the co-evolutionary information, as well as a small script to convert it into a Rosetta MathNTensor, and would like to add both scripts to the Rosetta tools directory.
These two scripts are necessary to be able to use our new mover and will be documented in the mover documentation.
Thanks to the GREMLIN creator Sergey Ovchinnikov who provided us with the code under a beerware license 🍻.
Hi there,
I am a new member of the Meiler Lab and for my master thesis I worked with Samuel Schmitz on using co-evolutionary information for protein design, derived from a multiple sequence alignment of homologous sequences with GREMLIN, to favor sequences which recapitulate correlated mutations as observed in nature. We also just submitted our paper (🎉), hoping that you can soon read about the results in detail.
We just merged the code to achieve this, see https://github.com/RosettaCommons/main/pull/4794 for details.
We used a slightly modified version of GREMLIN to generate the tensor storing the co-evolutionary information, as well as a small script to convert it into a Rosetta MathNTensor, and would like to add both scripts to the Rosetta tools directory. These two scripts are necessary to be able to use our new mover and will be documented in the mover documentation.
Thanks to the GREMLIN creator Sergey Ovchinnikov who provided us with the code under a beerware license 🍻.
Thanks for reviewing, Moritz