Today I will be talking about the second half of the Bioinformatics course and the individual project.
2) Structure Prediction
This part of the course also has both the theory and the Lab component. However, this half of the course is lab intensive unlike the previous one which was theory intensive.
This half has its own story. We start by learning about various structures and levels of protein organization. Then we proceed learn about the various types of secondary structures present and the type of interactions that keep them stable in their original conformation. From here we move on to various experimental and computational (main focus) methods of protein structure assignment and prediction. Structure prediction is of little help unless we use the structure to learn about its functions. To learn about functions, we then align the sequences and structure of this new protein to its homologs. These structures can then be experimentally verified using various techniques. We used the three dimensional structures present in the PDB database to perform various analysis such as modelling new proteins, modelling interactions, morphing, docking new molecules, which have applications in various academic as well as commercial fields.
Just like the first half of the course we had lab sessions that went hand in hand to the theory courses. The lab were much more interesting for most of us, as it was for the first time that we were looking at proteins and predicting their interactions and docking antibodies with antigens. However, as it was the first time handling such programs, most of which are command line based, we needed a lot of help which was provided by four TA’s. David, Sarah, Eloy and Marie, were very helpful in guiding us through the individual steps of the exercise personally. This improved our understanding exponentially.
As I had mentioned earlier that we also have an individual project for the course. Each of us is given a unique sequence of unknown origin. Our task is to find out everything about the sequence using all the tools and software that we have used so far in the lab. Thus, we start by finding the actual sequence by database search and then determine about its evolutionary origin using phylogenetics. Followed by its structure prediction and modelling the protein. To put it in short do everything we learned and apply on this particular new protein.
Finally, we had another partial exam for the second half of the course.
In general the course is very intensive and demanding. On a typical day, we dedicate at least 8 hours of which 5 hours is at the university and the remaining 3 for the assigned reading for the next day. Personally, I would say that this is the most cumbersome course so far in the MTLS masters, with 2 exams, an individual project, pre-lecture quizzes and the lab exercises all in a span of 5 weeks. However, we have learned a whole new field associated to biological sciences, and learn about what exactly does bioinformatics comprise apart from the data analysis and its domains that can stand independent to the experimental section.