We are 2020 iGEM team SJTU-BioX-Shanghai.
Here's our wiki homepage.
We have proposed a complete pipeline from a certain target sequence to Cas9/dCas9 variants with lower off-target effect. Models both guide the experimental process and evaluate the result of directed evolution. Researchers can use our off-target predictor to detect and select off-target sites with high confidence in experiments. Molecular dynamics method helps to find residues playing critical roles in interactions between DNA and Cas9/dCas9-sgRNA complex. The discovery of these functional positions integrates rational design into the directed evolution experiment. A graphic interpretation is also adopted to measure the mutation distance between different variants. On the other hand, our kinetics model fits the relationship between mismatch condition and off-target probability. The explainable parameters about transition state energy for WT Cas9 and evolved Cas9 can provide reliable inference on the changes in targeting progression after directed evolution.
Our model work is included in this repository: