In this course, sequence and structural bioinformatics will be seen in an integral way, which includes general bioinformatics, molecular modeling, immunoinformatics, docking and molecular dynamics, in addition to reviewing the concepts, the students will carry out the practice jointly with the teacher asynchronously.

PROGRAM

Module 1

General Bioinformatics

1. Motivation and Presentation

2. Computer Architecture

3. Operating Systems (Linux overview)

4. Introduction to Networks and Databases

5. Perl Programming for Bioinformatics

6. Bioinformatics exercises in Perl, review BioPerl

7. General concepts of Cell biology

8. Systematics and Evolution

9. Molecular Databases

10. Virtual Experimental Laboratory

11. Sequence Comparison

12. Sequence Comparison, Multiple Alignment, Molecular Phylogeny

13. Gene Identification

14. Analysis of Population Variation (SNPs)

Module 2

General Molecular Modeling

1. Description of amino acids: stereochemistry, nomenclature, physicochemical properties. 

2. Proteomics and OMICS

3. Immuno-informatics concepts

4. Biotechnology Fundamentals (microarrays)

5. Bioinformatics statistics 

6. Functional Groups, Atomic charges, conformation and configuration, LogP, Electronic and steric effects.

7. Chemical descriptors and QSAR 

8. Drug design considering properties ADMET, virtual screening, PCAs and Drug screening workflow systems 

9. Molecular mechanics (generalities) and Semi-empirical methods (generalities)

10. Quantum mechanics (general)

11. Protein-ligand docking 

12. Macromolecular-macromolecule docking 

13. Dendrimers, in silico studies.

14. Basic principles of molecular dynamics.

Module 3

Immunoinformatics

1. Innate and adaptive immunity

2. Peptide recognition by MHC 

3. MHC-Peptides-TCR

4. QSAR studies at MHC

5. Criteria for selection of antigenic protein

6. Sequence search and multiple alignment to obtain consensus sequence

7. Searches in databases of tertiary structures

8. Building and refining proteins

9. Evaluation of a tertiary structure

10. Prediction of linear epitopes and immunoproteosome

11. Conformational epitope prediction

12. Obtaining epitopes using protein-antibody complexes

13. Construction of the third dimension and structural refinement of epitopes

14. Coupling studies on MHC-I and MHCII

15. Dendrimers as peptide nanocarriers

16. Peptide-dendrimer coupling study

Module 4

Molecular docking

1. Presentation

2. Functional-groups-conformation-configuration

3. Physicochemical properties

4. ADMET Properties

5. Non-covalent-interactions

6. Scoring-Sampling-Function (energy exploration and calculation)

7. Preparation-Ligands-docking

8. Obtaining-target-for-docking

9. Install-autodock-adt-prepare-files

10. Continued-preparing-files for docking

11. Analysis of docking results

12. Continuation-analysis-docking-validation

13. Validation-docking

14. Final-docking-validation

15. FINAL ACTIVITY

Module 5

Molecular dynamics in protein

1. Presentation.

2. Protein structure.

3. Application of molecular dynamics (DM) in the pharmaceutical area.

4. DM application in the biotechnology area.

5. Generalities about Force fields.

6. Concepts, (RMSD, RMSF, Rg, solvent accessible surfaces, conformational changes).

7. Visualization exercises with VMD.

8. Files required for a DM.

9. Preparing files to run DM.

10. Structure minimization for DM.

11. DM simulation in NAMD.

12. Continuation of DM simulation at NAMD.

13. Analysis of results by VMD.

14. Analysis of results by CARMA.

Continuation of the analysis of results by CARMA and end of the module.