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Protein Design Primer: Principles and Tools for Protein Design and Engineering
Provider: Faculty of Health and Medical Sciences

Activity no.: 3194-26-00-00	There are 20 available seats
	Enrollment deadline: 01/08/2026

Date and time	31.08.2026, at: 16:00 - 07.12.2026, at: 18:00
Regular seats	20
Course fee	12,480.00 kr.
Lecturers	Nicholas Taylor
ECTS credits	4.70

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. Explain and utilize sequence-to-structure/function relationships in proteins 2. Apply computational and experimental methods for protein science and design 3. Understand the applications of protein design, e.g., in fundamental and applied research such as cell biology and healthcare 4. Start research in protein design Content This course will introduce protein design and engineering, cover the basics of protein chemistry, and provide a foundation in the theoretical background, applications, and practical implementation of computational and experimental protein-design tools for non-experts. This will allow CPD researchers to develop the underpinning knowledge and skills essential to initiate their research and for their future careers. In these ways, it will contribute to the democratization of protein design. Topics will include: • A brief history of protein design: from minimal to AI-based design • Introduction to PyMol • Sequence-to-structure/function relationships in proteins - Amino acids - Peptide bonds, conformational analysis and Ramachandran plots - Secondary structures and beyond • Computational and experimental methods for protein science and design - Contemporary protein modelling and computing tools, including PyMol, AlphaFold, Rosetta, RFDiffusion, ProteinMPNN, and other emerging methods and platforms - Molecular biology, protein expression and purification for protein production - Solution-phase characterization of protein structure and function; CD, fluorescence and NMR spectroscopy etc, AUC, etc - Protein crystallisation and X-ray crystallography, and cryo-electron microscopy • Discussion workshops on specific protein-design programmes - Rationally seeded protein design - Design of conformational transitions and switches - Design and delivery of supramolecular assemblies and vaccines - Targeting biological machines through de novo design Participants The course is designed for PhD students in the natural and medical sciences who lack a strong background in protein chemistry or prior exposure to protein design and engineering. The course is relevant for PhD students in programs in both SCIENCE and SUND (e.g., MoMed and DRA) faculties. Some Python scripting skills would be useful, but not mandatory, and a laptop is required for the course. 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 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. Practical sessions in the lab will also be included. 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: • Nicholas Taylor, Professor, Center for Protein Design (CPD), nicholas.taylor@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 Dek Woolfson, Professor, Center for Protein Design Tanja Kortemme, Professor, University of California, San Francisco Brian Kuhlman, Professor, University of North Carolina Nicholas Taylor, Professor, Department of Drug Design and Pharmacology Postdocs from the Center for Protein Design CPD Experimental Officer – a staff scientist with expertise in biophysics, currently being recruited to the Center for Protein Design Dates Mondays 31 August – 7 December 2026 and Tuesday 6 October 2026, 2–6 hrs per week contact time, so: Week 36-39: Mondays 16-18pm Week 40-44: Mondays 11-17pm Week 41: Tuesday 13-17 Week 45-50: 16-18pm No teaching in weeks 42 and 47 Course location Center for Protein Design University of Copenhagen Building 22, 4th floor Jagtvej 160 2100 Copenhagen Registration Please register before 1 August 2026 Expected frequency Annually in the autumn 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.

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