For the course in "Protein structure prediction of membrane and globular proteins" the main task is to do a project and a presentation on the same subject. In the project you will use your experience from earlier courses to develop a predictor for a "feature" of a globular or membrane protein. Please note that it is perfectly acceptable to talk about the project with other students, but that you are expected to write your code and work individually.
The following parts need to be fulfilled to pass the course
All project points should result in a (small) program written in python or any other language that can perform the supposed task. The data needed for your project as well as individual assignments will be given to you at the beginning of the course. The assistants will be available to help you with the assignments that happens this week. There will be very limited possibilities to get support with assignments from previous weeks, and there will be no support after the end of the course.
Please send a short (five line) summary before each thursday afternoon to Kristoffer. Below follows a schedule for your project.
Support is given at specific times and by email by sending an email to the firstname.lastname@example.org mailing list.
Here, the individual projects will be given out. A short description of the project will be given.
Your predictor has so far been based only on single amino acids. Your task is to improve the predictor by including A) a window of position-specific information and B) evolutionarily related sequence by using output from PSI-Blast
First, include the local sequence environment, by using different window sizes, i.e. to predict the feature for residue i and a window size 2k include the sequence information for all residues i-k to i+k.
How to run PSI-BLAST:
bash$ module add blast #This will add the blast module which contains PSI-BLAST in the program called "blastpgp" bash$ blastpgp - #This will bring up the blast help page #The profiles for the training data were generated by searching UNIREF90 with the following command bash$ blastpgp -b 0 -j 3 -h 0.001 -d /afs/pdc.kth.se/home/b/bjornw/Public/DB/uniref90.fasta -F F -i <fasta_file> -Q <profile>
Write one page about (1) your progress and (2) compare your method with previous work. Send it in an email to Kristoffer
PHP and mysql should be installed, if you need something else please contact the assistant(s).
The report, the program and the potential webserver all has to be submitted by Apr 29.
The final grade will be based on the quality of the report, and of the web-server written. If the project is not finished in time, the program does not work correctly or your report is not good enough you will fail. There will be a possibility to submit it again by Aug 20.
The grading will be based on the ability to do all assignments in time, the quality of the program and the written report.
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