Structural bioinformatics

A.Y. 2020/2021
Overall hours
BIO/10 BIO/11 FIS/07 INF/01
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.
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.
Course syllabus and organization

Single session

Lesson period
First semester
There are no differences in the program.
The teaching material will be available on Ariel.
Lectures and practicals will be online, asynchronous (including powerpoint with audio and notes) but regularly there will be a syncronous lecture to discuss the practical sessions.
The exam is unchanged and in case can be held online.
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
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.
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 ( 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 where 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 articles 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.
BIO/10 - BIOCHEMISTRY - University credits: 0
BIO/11 - MOLECULAR BIOLOGY - University credits: 0
FIS/07 - APPLIED PHYSICS - University credits: 0
INF/01 - INFORMATICS - University credits: 0
Practicals: 16 hours
Lectures: 40 hours
Professor: Camilloni Carlo
Educational website(s)