It is a course that will give you concepts and practice on primary, secondary and tertiary structure of proteins, you will learn to look for sequences, to use bioinformatics tools to build 3D structures. You will also learn concepts and use of tools to perform structural evaluation. The practice will be done by yourself on your computer with remote access to servers, installation of tools on your machine, etc.  

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TEMARY

Unit I: Introduction to protein prediction methods: (3 hours) (theoretical)

1. Biological aspects of proteins.

2. Classification of protein prediction techniques.

   1. Homology modeling

   2. Modeling by remote homology.

   3. Modeled by ab intio.

Unit II: Workshop on protein prediction techniques: (6 hours) (practical).

1. Alignments for the search for the crystal of the protein of interest.

2. Use of PDB databases.

3. Selection of the protein prediction technique.

4. Homology modeling prediction.

   1. Use of the Modeller program (Basic methods).

   2. Use of the Modeller program (intermediate methods).

   3. Use of the Modeller program (Advanced methods).

   4. Using the SwissModel server.

1. Prediction of iterative methods.

   1. Use of the I-Tasser program.

2. Protein prediction using ab-initio methods.

   1. Using the Robetta-Rosseta program

Unit III: Evaluation of the three-dimensional or quaternary structures predicted by the different methods: (3 hours) (practical).

1. Evaluation of the models by means of Ramachandra graphs.

2. Evaluation of the models by using ERRAT.

3. Evaluation of the models by means of VERIFY 3D.

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