Integrative Structural Bioinformatics
M.Sc. Program in Bioinformatics – Babeş-Bolyai University, Cluj-Napoca, Romania
Dr. Habil. Vlad Cojocaru
Principal Investigator/Senior Research Scientist
Babeş-Bolyai University/Utrecht University
Cluj-Napoca/Utrecht
Romania/Netherlands E-mail: vlad.cojocaru@ubbcluj.ro / v.cojocaru@uu.nl
Description
The aim of this course in to provide M.Sc students with a hand-on introduction to various computational approaches to study the structure and dynamics of biomolecular complexes at different scales (levels of detail). The focus will be mainly on the structure and dynamics of proteins and nucleic acids and their complexes. Special focus will be on building models of biomolecular complexes, predicting structures of biomolecular complexes, and running and analyzing molecular dynamics simulations of such complexes.
The course is designed as a research project aimed at answering a specific scientific question. It is composed of the following modules:
1. Visual analysis of biomolecular structures and their complexes
3. Building structural models based on experimental data
The course will be run on the NMRBox infrastructure NMR box.
The following software will be used:
At the end of the course, the students will have an understanding of how to use computational resources to answer fundamental questions in computational structural biology and biochemistry. In particular, the students will be able to: (1.) visually analyse structures of biomolecules, (2.) build structural models of proteins and protein-DNA complexes, (3.) setup and perform molecular modelling and simulations, (4.) visualize and analyze molecular dynamics simulation trajectories, (5.) dock biomolecules to predict their interactions, (6.) set up and complete a research project, (7.) write a report on the performed project, and (8.) present a prestigious research article.