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Institución:Instituto Biologia Molecular Barcelona CSIC Contacto correo-e:uson@ibmb.csic.es
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Call: PreDoc FPI – Formación Personal Investigador MdM 4-year contract from the Spanish Ministry of Economy and Competitiveness.
Qualification: Last year degree- or master student in computer science, mathematics, physics, chemistry, biochemistry or biotechnology with programming knowledge (python or other).
The Crystallographic Methods group at the Maria de Maeztu Excellence Unit of the Department of Structural Biology at the IBMB-CSIC (Barcelona Science Park, www.pcb.ub.edu), seeks a Master or Degree student to carry out an interdisciplinary project in the development of computing methods in Structural Biology within our software ARCIMBOLDO (http://chango.ibmb.csic.es/
http://www.ibmb.csic.es/index.
Predicting protein folding from the amino acid sequence remains one of the missing holy grails of biology. After five decades of protein crystallography, we have achieved the three-dimensional characterization of over 100.000 macromolecular structures. Structure has shed unique insight into manifold biological questions, but despite the wealth of information gathered in the PDB database, our understanding of its essence is insufficient: we usually get an insight into the relation between the function and the geometry for a small part of the structure, regarding active or binding sites, etc… and as for understanding folding itself, our success in de novo prediction is very limited and at best uncertain.
The paradigm is shifting, blending detailed investigation of specialized aspects into global apprehension of complex systems. We need a tool to understand fold in its full scope. In analogy to Borges’ story, an Aleph, a point in space that contains all other points. Anyone who gazes into it can see everything in the universe from every angle simultaneously, without distortion, overlapping or confusion.
In the field of crystallographic ab initio phasing we have developed within our program ARCIMBOLDO a successful algorithm for the extraction of tertiary structure constraints from all the structures in the PDB. It is based on the geometrical expression of polypeptide conformation through characteristic vectors, affording detailed and customizable analysis of main chain geometry and of the spatial relationship among structural elements.
Characteristic vectors and supercomputing will be the base of our particular Aleph, to explore local folds of noncontiguous protein fragments with a customizable level of detail and through them reconstitute the whole fold so as to simultaneously apprehend a detailed and an overall view. We want to probe our new algorithm to explore, through local fold, the problems of phasing, folding, functional interactions and lattice formation.
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Información complementaria de la oferta:
Information on our programs and publications can be read from our web:
http://chango.ibmb.csic.es/
Interested applicants, should contact ICREA Res. Prof. Isabel Usón (uson@ibmb.csic.es), with an academic CV (detailing subjects and marks) and cover letter describing motivation and contact details for one or two potential references.
