Structural Bioinformatics
A.Y. 2023/2024
Learning objectives
The aim of the course is to provide students a thorough overview of the computational tools, and some of the underlying theory, to study the dynamics of biomolecules by computer simulation techniques. The course covers progresses in the development of atomistic, coarse-grained and quantum mechanical simulations and expand on methods for structure predictions based on statistical and evolutionary data and on hybrid methods that integrate structural biology techniques (Nuclear Magnetic Resonance, Small Angles X-Ray scattering, Cryo-electron microscopy) and computer simulations to increase the accuracy of computer simulations and experiments.
The course is ideally linked to those dealing with protein engineering and structural biology.
The course is ideally linked to those dealing with protein engineering and structural biology.
Expected learning outcomes
After following this course, students will know how computer simulations of biomolecules can be used to investigate biological problems at the molecular level.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
The course is focused on the use of computer simulations to investigate the structure and dynamics of biomolecules (proteins, nucleic acids, and membranes). Each topic will be introduced theoretically and then learned hands-on using state-of-the-art software. Topics include: analyzing, visualizing, and comparing protein structures and trajectories; protein structure predictions and docking; molecular dynamics simulations (atomistic and coarse-grained); quantum chemistry simulations; free energy methods and protein design approaches. During the course, the students will have the opportunity to learn how to use a Unix terminal and to manage data using Python notebooks.
Prerequisites for admission
None.
Teaching methods
Teaching mode: 2/5: classroom lectures supported by projected material; 3/5 practical sessions in the computer lab.
Attendance: compulsory for practical sessions, highly recommended for classroom lectures.
Attendance: compulsory for practical sessions, highly recommended for classroom lectures.
Teaching Resources
Computer simulations of liquids (2nd edition). D. J. Tildesley and M.P. Allen (Oxford)
Statistical physics of biomolecules, an introduction. Zuckermann (CRC press)
Copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano (https://ccamillonisb.ariel.ctu.unimi.it/v5/home/Default.aspx). By no means this material replaces the lectures or a textbook. The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others.
Statistical physics of biomolecules, an introduction. Zuckermann (CRC press)
Copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano (https://ccamillonisb.ariel.ctu.unimi.it/v5/home/Default.aspx). By no means this material replaces the lectures or a textbook. The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others.
Assessment methods and Criteria
The evaluation of the student's performance is based on an oral examination. The student will present a scientific article where one or more of the techniques presented in the course have been used to tackle a biological problem. Furthermore, during the course, students will redact a report of the practical activities and the report will be used to discuss one of such practical experiences. This examination allows students to test their ability in understanding scientific literature based on the techniques learned during the course and to verify their practical understanding of the topic covered.
Examples of the examination test will be discussed during classes and made available to students.
Examples of the examination test will be discussed during classes and made available to students.
BIO/10 - BIOCHEMISTRY
BIO/11 - MOLECULAR BIOLOGY
FIS/07 - APPLIED PHYSICS
INF/01 - INFORMATICS
BIO/11 - MOLECULAR BIOLOGY
FIS/07 - APPLIED PHYSICS
INF/01 - INFORMATICS
Practicals: 16 hours
Lectures: 40 hours
Lectures: 40 hours
Professor:
Camilloni Carlo
Professor(s)