Due to the coronavirus situation, the 2nd part of this course will be held remotely in week 18 (beginning April 27th). Contact the course responsible with questions.
Dates: Bergen week 10 ( 2-6. March) and Tromsø, week 14 (30. March-3.April) 2020
Place: Realfagbygget, UiB (the first week) and Institute for Chemistry, UiT (the second week)
Course responsible: Nathalie Reuter (UiB)
Exam: Oral exam, tentatively May 2020 (might be over a video system/Skype)
Credits: 10 ECTS
Registration: Deadline 12.02.2020
The course will present central methods in molecular modeling for the analysis of enzyme structure-function relationship and the modeling of their catalytic activity.
The course will be given over two weeks from 9 to 16 every day, not necessarily consecutive, and happening on two different sites (UiB and UiT). Mornings will be dedicated to lectures (3 hours) and afternoons to hands-on sessions (4 hours).
D1: Computational methods for the investigation of structure-function relationships of enzymes
D2: Force fields (FF)
D3: Geometry optimization/Molecular simulations
D4: Enhanced sampling methods
D5: Normal mode analysis
WEEK 2 (35 hours lectures+hands on)
D2: Free energy calculations
D3: Empirical Valence Bond (EVB)
D4: Quantum mechanical calculations for the purpose of FF/EVD parameterization
D5: Validation of computer simulations
The students will be given two independent assignments to work on. One will focus on the learning outcomes from week #1 and the other one on the projects from week #2. Each project will require that the students perform computations on their own and will be independent of the exercises done during the hands-on session. We estimate that each project will require about 3-5 days of work
Exam and evaluation
Assignments will count for 50% of the final evaluation. Oral exam will count for the other half (might be over a video conferencing system)