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>

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.

Quantitative analysis