Admission Requirements
Core course in MSc Chemistry – Chemical Biology. Elective course for MSc Life Science and Technology, MSc Chemistry – Energy & Sustainability and MSc Bio-Pharmaceutical Sciences.
Required background knowledge is thorough knowledge of protein structure and organic chemistry at the level of Organic Chemistry 2 (4052ORGC2 for BSc MST, LB2301 for BSc LST or equivalent).
Description
Although chemical biological research is typically viewed as a purely empirical endeavour, computational techniques can be of tremendous help in explaining and predicting observations made.
In this course, students will be introduced to a broad set of computational approaches used in chemical biology. Topics include: calculating and analysing physicochemical properties of large sets of compounds (cheminformatics), finding and using online repositories of published data, running and analysing molecular dynamics simulations on proteins, quantum mechanical approaches to conformation analysis and finally structure based drug discovery and machine learning applications to drug discovery.
This course aims to:
raise students’ interest and enthusiasm for the field of computational chemical biology.
give an introduction of the most important concepts and computational methods used and their application in chemical biology and drug discovery.
give the student sufficient background to interpret computational methods and fundamental approaches found in chemical biology research publications.
introduce a number of public databases that are relevant for computational chemical biology.
explain limitations in cheminformatics, bioinformatics or computational chemical biology.
introduce the latest developments and insights in the field of machine learning and drug discovery.
allow students to solve problems that are rooted in the biological domain with computational tools.
Course objectives
After the course, students will:
be able to apply important principles of chemical informatics;
understand the basic principles governing the physicochemical properties of molecules;
be able to explain the benefits and limitations of computational techniques as applied in chemical biology;
be able to set up a molecular dynamics simulation for a protein and analyse the results;
understand the fundamental differences between molecular mechanics force fields and quantum-mechanical calculations and when to apply which;
have a basic understanding of structure-based drug discovery and the most important subdisciplines thereof;
have a basic understanding of artificial intelligence methods as it is applied in drug discovery.
Timetable
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
Mode of Instruction
The course will use a combination of lectures (typically 4-6 hours per week) and hands-on computer work (typically 2-4 hours per week, usually after the lectures). A laptop running Windows, Linux or Macintosh operating system is required, see below. In case of ongoing restrictions in group size or university access, online alternatives will be used to organise lectures and working groups.
Assessment method
A written exam will make up the final grade (100%).
Presence and active participation during the working groups (mainly computer assignments) and discussions is mandatory to be admitted to the exam and retake.
Reading list
Literature will be provided during the course via Brightspace.
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Dr. Anthe Janssen, Dr. F. Buda, Dr. W. Jespers
Remarks
Assignment deadlines are communicated via Brightspace.
A relatively young laptop (2014 onwards) running Windows, Linux or Macintosh operating system is required.
Only 64-bit processors are supported, not ARM. This means:
Macs with Apple Silicon (MacBook Pro (13-inch, M1, 2020), MacBook Pro (14-inch, 2021), MacBook Pro (16-inch, 2021), MacBook Air (M1, 2020) and later models) are not supported.
Windows laptops with Snapdragon processors (2024 and later) are not supported.
According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.