Biomolecules Folding and Disease

The course Laboratory of Bioinformatics 1 (66563) includes in the second semester a 60-hour module given by Emidio Capriotti. Only few students brave students remianed until the lst minute The module was running from March 3 to April 15, 2025 and the lectures were given in Via dell Beverara 123/1. Only few brave students remained until the very last moments of the course (see picture). The teaching channel of the LM Bioinformatics is accessible through the following link. The recordings of the lectures are be accessible through the vituale platform. This page include all the slides and materials of the course.

• Materials
  

  Course Schedule
  Introduction and Basic Concepts	3 March, 2025.
  Protein and RNA Structure Alignment	4, 6 an 10 March, 2025.
  Multiple Alignments	11, 13 and 14 March, 2025.
  Probabilistic Models for Biological Sequences	17 and 18 March, 2025.
  Hidden Markov Models	20 March, 2025.
  HMM for Sequence Alignment	24 March, 2025.
  HMMER	25 March, 2025.
  Introduction to the Project and Implementation of a Blast-based Method.	28 March - 1 April 2025.
  Project Implementation	3-8 April, 2025.
  Protein Structure Analysis	10 April, 2025.
  Protein Structure Prediction	14 April, 2025.
  Predicting the effect of protein variants	15 April, 2025.
  Hands-On Programming Sessions




• Requirements
  

This is a theoretical 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
  

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

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

Sviatopolk-Mirsky Pais et al. Assessing the efficiency of multiple sequence alignment programs. Algorithms for Molecular Biology, 2014.

El-Gebali et al. The Pfam protein families database in 2019. Nucleic Acids Research, 2019.

Loewenstein et al. Protein function annotation by homology-based inference. Genome Biology, 2009.

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




• Previous Editions
  

March 2024:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 4 March to 30 April, 2024. More information is available at this link.
March 2023:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 6 March to 26 April, 2023. More information is available at this link.
March 2022:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 8 March to 26 April, 2022. More information is available at this link.
March 2021:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 9 March to 30 April, 2021. More information is available at this link.
March 2020:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 10 March to 30 April, 2020. More information is available at this link.
March 2019:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 12 March to 17 April, 2019. More information is available at this link.
March 2018:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 13 March to 3 May, 2018. More information is available at this link.
March 2017:	The Module 2 of the Laboratory of Bioinformatics 1 was held from 13 March to 4 May, 2017. More information is available at this link.