• 8:00 a.m. a 9:00 a.m: Inscription
  
  
• 9:00 a.m. a 9:30 a.m: (Inauguration) Words of the Dra. Olga Márquez and Dr. José Luis Ramírez
  
  
• 9:30 a.m. a 12:00 m: "Structure of peptide - immune molecule complexes: the basis for T and B cell epitope predictions" by Johan Hoebeke
  
  Resumen: The structure of peptide-HLA and peptide-MHC class I and class II complexes will be discussed together with a few examples of MHC - peptide - T cell receptor complexes. The potential to use these data for T cell epitope prediction will be advanced. An overview of the structure of B cell epitopes - neutralising antibodies will be given. Possibilities to determine neutralising B cell epitopes and to model peptide - antibody complexes will be discussed.
  

Afternoon:

• 2:30 p.m. a 3:30 p.m: "QSAR y Similaridad Molecular para el diseño de Farmacos" by Luis Rincon

Resumen: Abstract: A general overview on molecular similarity and applications to QSAR is presented. The procedure for molecular alignment and statistical analysis are presented and complemented with examples. The similarity measures were used to estimate dissociation constant for acid-base equilibria, and in the benchmark problem of steroid binding affinity. In the second part of this conference, Molecular Similarity QSAR analysis of some eter derivaties of didydroartemisin has been performed in an attempt to explore the parts of the molecule that are most important for the mediation of the activity. This study reveals the importance of peroxide bridge of artemisin skeletal.

• 3:50 p.m. a 5:50 p.m: Practices at CEIDIS
by José David Rosales

• 8:00 a.m. a 9:00 a.m: Inscription
  
  
• 9:00 a.m. a 12:00 m: "Molecular evolutionary studies in Public Health: from drug resistance to vaccine design" by Ananias A. Escalante
  
  Resumen: The use of evolutionary biology concepts in public health will be discussed. Three problems will be addressed (1) the use of molecular markers in molecular epidemiologic investigations, (2) assessing the genetic diversity of antigens for vaccine development and (3) the origin and dispersion of drug resistance. These problems will be discussed using malaria as an example. The need for longitudinal studies will be presented for investigating parasite population structure, the relevance of inbreeding and complexity of infections in the context of Public Health. Finally, the need of portals, where bioinformatics and epidemiologic tools are integrated, will be discussed as a strategy to support global health initiatives.

• 2:30 p.m. a 3:30 p.m: "Diagnostic of Needed bioinformatic tools necessary for the development of Latinoamerica genomics" by José Luis Ramírez
  
  Resumen: In Latin America ample support has been given to the use of bioinformatics in philogenetic and population studies, and the teaching of basic tools for sequence analysis. However, except for Brazil, most countries lack of human resources able to attack: intermediate sequence assembly projects; datamining in search of proteins or function prediction; high-output technologies data processing etc., Here I revise some of these technologies and propose the establishment of at least three focal points where these type of resources are ready available for Latin American researchers

• 3:50 p.m. a 5:50 p.m: Practices at CEIDIS by José David Rosales

• 9:00 a.m. a 12:00 m: "Statistical simulations of biological systems. Characterization, problems and pitfalls along the gilded road" by Chris Chipot

Resumen: Recent developments on both the hardware and the software fronts have made possible "state-of-the-art" statistical simulations of large collections of atoms, that explore in apt thermo-dynamic ensembles a significant range of the phase space, within a reasonable time frame.1 Molecular dynamics simulations targeted at the investigation of physical and chemical phenomena in complex, biologically realistic molecular assemblies constitute an area that has gained from these developments because of the inherent slow relaxation involved in such systems, requiring a sizeable computational effort to yield converged properties. Because molecular dynamics unquestionably represents a powerful tool capable of supplying the microscopic detail that experiment cannot always capture, characterization of the metho-dology and its underlying principles is pivotal to appreciate the field of applications it embraces, as well as its intrinsic limitations.

This presentation is an opportunity for a critical look at the arsenal of methods currently available to access both thermodynamic and dynamic information in large biomolecular systems. After describing the contemporary algorithms utilized in large-scale molecular dynamics simulations2 - e.g. propagator, long-range electrostatic interactions and multiple time-step - the results for a selection of biologically relevant problems will be discussed. Of particular interest, the interaction of cholesterol with a fully hydrated lipid bilayer,3 the self-assembled cyclic peptides that form hollow cylindrical structures integral to the cell membrane, capable of modulating the permeability properties of the latter,4 and the resting state of the Shaker B voltage-gated K+ channel in a lipid environment5 will be presented. In addition, free energy calculations, which constitute a tangible, quantitative link with experiment,6 will be reported for a variety of problems including protein-ligand associa-tion,7drug delivery across the cell membrane,8 and oligomerization of transmembrane a-helical domains.9

This set of applications that take advantage of massively parallel architectures, demonstrates the usefulness of molecular dynamics simulations to advance our ability to explain key-properties of the cell machinery. While highlighting the progress made in recent years - the result of relentless efforts to push back the limits of statistical simulations in order to tackle large, realistic and biologically relevant molecular assemblies - it also underlines the efforts still to be made to circumvent the current pitfalls on the road to model increasingly complex biological systems.

• 2:30 p.m. a 3:30 p.m: "Molecular Dynamics simulations of Haemagglutinin of Influenza Virus" by Raul Isea

  Resumen: Haemagglutinin (HA) is responsible for influenza infection in humans. It is known that HA is implicated in the binding process between the virus and receptors cells before the infection, which is necessary for the release of the viral genome into the cell. So in the light of the above facts, it is extremely important to understand the conformation of this glycoprotein. The crystal structure of Haemagglutinin has been determined by X-ray experiment. Based on them, molecular dynamics (MD) simulations were performed using the Charmm software package. The simulation showed that HA is extremely mobile. This result could explain how the protein is able to find the sialic acid containing host cell receptor, and maybe, this is the main reason for the difficulty in producing an effective vaccine against influenza.

• 3:50 p.m. a 5:50 p.m: Practices at CEIDIS by José David Rosales

• 9:00 a.m. a 12:00 m: "Bioinformants: Intelligent tools for bioinformatics" by Jacinto Davila
  
  Resumen: Bioinformants is a software to integrate a number of bioinformatics tools and enable them for the Web. It is aimed to add intelligence (in the sense of flexibility and user-friendlyness) to existing programs to analyze genetic information, by means of techniques drawn from Artificial Intelligence. Agents and logic-based data mining, in particular, are used as the building blocks of the integrated environment of Bioinformants.

• 2:30 p.m. a 5:30 p.m: "Annotation and metabolic reconstruction of microbial genomes: putting genomes to work" by Dr. David Holmes

• 9:00 a.m. a 12:00 m: "Sequence annotation and applied genomics" by Wim Degrave
  
  Resumen: Assembly of a sequenced genome and analysis of its content involves both automated ("first round") and semi-automated ("second round") annotation of sequence features, such as ORF analysis, structural RNA localization, analysis of repetitive sequences and transposons, promoter and replicon analysis, and tentative functional classification of predicted proteins. Further in-depth annotation is needed to extract relevant features and to prepare for applied genomics developments such as the identifcation of new diagnostic tools, new vaccine and drug candidates etc. Other bioinformatic tools for comparative genome analysis are also available, but preferrably distributed input of specialists in the biology of the organism is badly needed in this phase. Different tools and approaches will be discussed and demonstrated.

• 2:30 p.m. a 6:30 p.m: Excursion and visits observatory CIDA