Binder design is often formulated as “given a target protein (and optionally a specific epitope on that protein), design a (often smaller) protein capable of binding the target”. It is one of the most ubiquitous protein design problems and has many potential applications, largely functioning by blocking or competing with natural interactions involving the target protein.
In this bootcamp, you’ll have the opportunity to explore the computational binder design problem across three different categories of targets. Students will choose from a curated list of targets that have been validated with BindCraft and other computational binder design tools.
Students will select a target from the list above (4 students per target). Each student will work on the project individually and as a group throughout the week. As we learn about each tool, you’ll have time to explore how that tool works for your particular protein. Be sure to make note of any quirks or nuances related to your protein, e.g. any particular settings used or any issues encountered.
At the end of the week, all students who were assigned the same target will reconvene and create a presentation that summarizes results, findings, and observations related to the target. We recommend creating a shared Google Drive folder and a shared documentation file (lab notebook style) to contain predictions, results, settings tried, and commands used so that you can easily refer to them when making the final presentation.
The goals of this project are as follows: