> For the complete documentation index, see [llms.txt](https://amo-ai.gitbook.io/amo/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://amo-ai.gitbook.io/amo/protein-evolution-design-folding/protein-design.md).

# Protein design

This project aims to provide a computational method for protein design. Accordingly, we can design a \`\`super protein" of a protein family stabilizing in a large range of temperature.

## Single mutation

Leri provides a tool, shown as following command, for the computer-aided design of mutant proteins with controlled evolutionary information. It evaluates the changes at signle site in stability of a protein without referring to its tertiary structure. Figure 1 illustrates energy changes ( $${\Delta}E=E\_{mut}-E\_{wt}$$) between wild type and mutant sequences when a single mutation occurs to the wild type sequence of ww-domain protein.

```
amo point_mutation \
-jobname <STRING> \
-fastx <STRING> \
-mat <STRING>
```

![](https://1482538969-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-Lm6CWff_Qq7mC9Nt6ol%2F-LmEez7jb_Zf3Mq9-uRj%2F-LmEfB9OnUeDdZvpl1WX%2FGPCR2RH1_WT_r_point_mutation.png?alt=media\&token=87dfb8cb-abc4-416b-9301-35a225413ba5)

## Coupled mutation

```
amo sequence_design \
-fastx <STRING> \      # wild-type sequence in FASTA
-mat <STRING>          # potentials for sequences in the family
-temperature <FLOAT> \ # temperature
-n <INT> \             # number of mutants
-max_iter <INT>        # maximum number of iterations
```

## Protein design

Leri can be applied to facilitate the design of a given WT protein, and it attempts to uncover the biophysical rules (evolutionary information) that govern protein folding.

![](https://1482538969-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-Lm6CWff_Qq7mC9Nt6ol%2F-LmBnAHxYGE4VGpRuex8%2F-LmBpFdEbho4s_J8vysL%2FDEE_steps.png?alt=media\&token=7ba3a68f-5b66-46b4-a559-f48ed320b63b)

## Quantitative analysis

![](https://1482538969-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-Lm6CWff_Qq7mC9Nt6ol%2F-LmBnAHxYGE4VGpRuex8%2F-LmBq2VZ_UmTfO17gLda%2FGPCR_coupling_cleaned_matrix_sector.png?alt=media\&token=7cbc9c8e-eb99-4765-9da6-a5ed08289cb5)