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University of Parma
Course catalogue
Università degli Studi di Parma
course catalogue

BIOINFORMATICS
cod. 13558

Academic year 2008/09
3° year of course - First semester
Professor
Academic discipline
Fisica applicata (a beni culturali, ambientali, biologia e medicina) (FIS/07)
Field
Ambito aggregato per crediti di sede
Type of training activity
Hub-specific activity
24 hours
of face-to-face activities
3 credits
hub:
course unit
in - - -
lectures timetable unavailable
exam calls
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Learning objectives

To provide the students with the basic concepts and tools of the structural bioinformatics, from the sequence analysis, to the protein modelling and the computer simulations of molecular dynamics and interactions.

Prerequisites

Basic knowledge of macromolecular structures.

Course unit content

Sequence analysis : databases search for sequence and structures of nucleic acids and proteins; protein sequence identification from DNA fragments; automatic sequence comparation by means of softwares based on the recognition of high local similarity regions; recognition and analysis of characteristic patterns in the sequences; pairwise and multiple sequence alignments; protein secondary structure prediction from the primary sequence; protein physico-chemical profiles. Tertiary structure of proteins: use of molecular graphics and analysis softwares. Building of three-dimensional models of non-crystallized proteins at atomic detail, by means of the comparative modelling approach. Fold recognition and prediction methods. Energy minimization. Introduction to the molecular dynamics simulations and their applications. Introduction to the docking simulations for the study of the interaction between proteins and ligands.  

Full programme

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Bibliography

A.M. Lesk, "Introduzione alla Bioinformatica", McGraw-Hill Ed. <br />
G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole, "Introduzione alla Bioinformatica", Zanichelli Ed. <br />
D.E. Krane, M.L. Raymer, "Fondamenti di Bioinformatica", Pearson Education Ed. <br />
A. Tramontano, Integral and differential form of the protein folding problem, Physics of Life Reviews, 1:103-127 (2004). <br />
W. L. Jorgensen, The many roles of computation in drug discovery, Science, 303:1813-1849 (2004). <br />
Notes on the lessons will be given by the lecturer. <br />

Teaching methods

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Assessment methods and criteria

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Other information

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