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3rd Diploma in Bioinformatics, Immunoinformatics and Molecular Modeling


Duration: 4.5 months


Course start: January 10, 2022


Modality: Online


Spanish Language

about the DIPLOMA

Temario actualizado
en proceso de registro en STPS y SEP-CONOCER

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.




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


  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


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.

What will you learn

Molecular dynamics


Structural bioinformatics


of sequences

Coming soon  your

 The material provided was consistent with what was seen in the video classes. In fact, in the chat forum, it was enriched by the questions of the participants where, based on these doubts, other links and / or other articles were suggested
Rosa Cardenas

Investment $ 5,500 MN

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