PhD course: Advanced Methods in Protein Design

Advanced Methods in Protein Design: Computational and Experimental
Tools for Contemporary Protein Design Applications

This course will refresh your knowledge of the key fundamental principles and foundational concepts of protein design. It will then move quickly onto contemporary approaches, challenges, and applications in this rapidly advancing field. Specifically, it will cover rational, physics-based computational, AI, and combined approaches to protein design. In the sessions, you will learn how to construct algorithms for protein design and use off-the-shelf protein-design software. However, this will not be a course in coding per se. Next, you will learn how to apply protein design through sessions on contextualized protein design and responsible research and innovation. By the end of the course, you will be equipped with sufficient knowledge to develop your own projects and protein-design pipelines, and to apply these in fundamental or applied research.

Topics will include: 

  • Advanced computational methods in protein design, including programming
  • Rational design methods as exemplified by de novo coiled-coil peptides and proteins
  • Physics-based methods as exemplified by Rosetta and others
  • Generative AI I: structure-based methods
  • Generative AI II: protein large language models (pLLMs)
  • Contextualised protein design, including:
    advanced screening/selection methodologies
    designing proteins for extreme conditions
    designing proteins for cellular environments
  • Designing protein complexes and complex functions:
    small-molecule and macromolecule binding proteins
    dynamic proteins and molecular switches
  • Designing motor proteins
  • Ethical issues in protein design, and responsible research and innovation
  • Translation and Innovation in Protein Design
  • Advanced topics in protein design given by CPD Core & Associate staff and CPD Laureates
     

Lectures will be combined with student-centered, problem-based, and discussion-focused learning. Advance reading prior to the in-person session will allow for the session time to be used for working through foundational and contemporary examples and for discussion.

Registration is open! The registration deadline is 3 January 2027.