BioFolD - Emidio Capriotti

Biomolecules Folding and Disease

Laboratory of Bioinformatics I - Module 2

The course Laboratory of Bioinformatics 1 (66563) includes in the second semester a 60-hours module given by Emidio Capriotti. The course director is Prof. Rita Casadio. The module is running from March 13 to May 4, 2017 in the Laboratory of Bioinformatics at the ground floor of Via San Giacomo 9/2 (back entrance). This page will include all the slides and materials of the lectures.

Materials

Course Schedule
Introduction and Basic Concepts	March 13, 2017.
Protein Structure Alignment	March 14 and 16, 2017.
Multiple Alignments	March 20 and 21, 2017.
Hidden Markov Models	March 23, 2017.
HMM Alignments	March 27, 2017.
HMMER	March 28 and 30, 2017.
Introduction to the Project	April 3,4 and 6 2017.
Project Implementation	April 10,11,20 and 21 2017.
Protein Structure Prediction	April 27 and 28 2017.
Structure Analysis and Variants	May 2 2017.
Predicting the Effect of Protein Variants	May 4 2017.

Requirements

This is a theoric and hands-on module which requires the use of PC. Students need to use their own laptop. Practical session of the course will be performed on a Linux OS.

References

Structural Bioinformatics II Edition: Structural Comparison and Alignment.
by Marti-Renom et al.

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives. PLOS ONE, 2011.
by Thompson et al.

Pfam: the protein families database. Nucleic Acids Research, 2014.
by Finn et al.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics, 2012.
by Xu and Dunbrack.

Evaluation

In this page we included the evaluation form anonymously compiled by the participants to evaluate the quality of our course. Answers submitted with numbers from 1 (No) to 4 (Yes) have been included in the following statistics calculated by R. The evaluation form was compiled by 11 participants which rated the course with an average score of 3.5 over 4. The received positive and negative comments will be published soon.

Data