Graduate School of health and Medical Sciences

Login for PhD students at UCPH Login for others

Advanced Methods in Protein Design
Provider: Faculty of Health and Medical Sciences

Activity no.: 3197-27-00-00	There are 20 available seats
	Enrollment deadline: 03/01/2027

Date and time	01.02.2027, at: 09:00 - 12.02.2027, at: 17:00
Regular seats	20
Course fee	16,080.00 kr.
Lecturers	Joseph Rogers
ECTS credits	8.10

Contact person	Marianne W. Jørgensen E-mail address: marianne.joergensen@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration SUND E-mail address: phdkursus@sund.ku.dk

Enrolment guidelines This is a specialised course. This means that 80% of the seats are reserved to PhD students enrolled at the Faculty of Health and Medical Sciences at UCPH and 20% of the seats are reserved to PhD students from other Danish Universities/faculties (except CBS). The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. Articulate and discuss the contemporary approaches and challenges in de novo protein design. 2. Make informed decisions on the best protein-design approach – rational, physics-based computational, AI, or combined approaches – for a given research problem. 3. Construct algorithms for protein-design programmes, and apply off-the-shelf protein-design software to deliver these. 4. Develop your own projects and protein-design pipelines, and apply these in fundamental or applied research. Content This course will refresh your knowledge in 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, students 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: o advanced screening/selection methodologies o designing proteins for extreme conditions o designing proteins for cellular environments • Designing protein complexes and complex functions: o small-molecule and macromolecule binding proteins o 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 Participants The course is designed for PhD students in the natural and medical sciences who have taken the UCPH Protein Design Primer PhD course or who are well-trained in peptide/protein chemistry (typically an MSc in Biochemistry, Chemistry, or Medicinal Chemistry). Python scripting and unix command line interface skills and a laptop are required for the course. The course is relevant for PhD students in programs in both SCIENCE and SUND (e.g., MoMed and DRA) faculties. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: - All graduate programmes We included “All graduate programmes” because there might be students in many different programmes whose research is related to protein design or who have a strong motivation to learn. Language English Form Lectures are combined with student-centered, problem-based, and discussion-focused learning. Course instruction will use Flipped Learning, with the participants being asked to prepare a small amount of work ahead of interactive sessions of various formats, e.g., quiz-style exercises on protein chemistry with students working in pairs at whiteboards; reading a relevant section of a textbook, a paper, or a review article ahead of group discussions; writing a piece of code for testing and improving in a workshop; or preparing short presentations on advanced topics. This format will facilitate assessment, which will be done alongside the classes. Advance reading prior to the in-person session will allow for the session time to be used for working through examples and for discussion. Course director Course directors: • Joe Rogers, Associate Professor, Center for Protein Design (CPD), joseph.rogers@sund.ku.dk • Dek Woolfson, Professor, Center for Protein Design (CPD), d.n.woolfson@bio.ku.dk Course coordinator: Gretchen Repasky, Center Scientific Manager, Center for Protein Design, gretchen.repasky@bio.ku.dk Instructors Amelie Stein, Professor, Department of Biology, University of Copenhagen Birthe Höcker, Professor, University of Bayreuth (DE) BM - Bram Mylemans, Postdoc, Center for Protein Design, University of Copenhagen CN - Christoffer Norn, Co-founder & CEO, Skape Bio (DK) DNW - Dek Woolfson, Professor, Center for Protein Design, University of Copenhagen JR - Joseph Rogers, Associate Professor, Center for Protein Design, University of Copenhagen KJJ - Knud Jensen, Professor, Department of Chemistry, University of Copenhagen TJ - Timothy Jenkins, Professor, Technical University of Denmark (DK) Dates Weeks 5 and 6 in 2027. See course program for details. Course location Center for Protein Design University of Copenhagen Building 22, 4th floor Jagtvej 160 2100 Copenhagen Registration Please register before 3 January 2027 Expected frequency Annually in the late winter/early spring Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment.

Click the search button to search Courses.

See which courses you can attend and when

Jan	Feb	Mar	Apr
May	Jun	Jul	Aug
Sep	Oct	Nov	Dec