Coordinator: Prof. S. Hamodrakas

Lecturers: Prof. S. Hamodrakas | Assoc. Prof. G. Rodakis | Dr. I. Almyrantis | Dr. P. Bagos | Dr. V. Oikonomidou

• Introduction: DNA and protein sequences
• Sequence similarity search algorithms: Sequence homology and similarity and their importance, dynamic programming algorithms, Global Alignment and Needleman & Wunch algorithm, Local Alignment and Smith & Waterman algorithm, Calculation of alignment's statistical significance, Importance of Identity matrixes, gaps and penalties, Heuristics methods for similarity searches in databases (BLAST, FASTA etc).
• Multiple sequence alignment: Multidimensional dynamic programming algorithms, Heuristic methods for multiple sequence alignments (HMMER, SAM, HMM-Pro etc), phylogenetic trees and multiple alignments
• Discovery of patterns and periodicities in protein and DNA sequences
• Prediction algorithms based on protein and DNA sequences: Empirical statistical methods, Clustering, Neural networks, Ηidden Markov Models, Genetic algorithms. Applications of the above mentioned methods for:
  • Secondary structure prediction of proteins and RNA
  • Prediction of Transmembrane segments and their orientation in proteins
  • Gene finding in DNA sequences
  • Multiple sequence alignments using Hidden Markov Models (HMMER, SAM, HMM-Pro etc)
  • Sequence clustering in families

2.  Computational Analysis of Biomacromolacular Structures

Coordinator: Prof. E. Iliopoulos

Lecturers: Prof. S. Hamodrakas | Prof. E. Iliopoulos | Dr. M Vlasi | Dr. N. Papandreou | Dr. V. Oikonomidou

• Introduction - Biomolecular structures - Determination methods
• Fold recognition
• Fitting (Anteposition) of stereo structures
• Comparative homology modeling - Threading
• Modelling of protein structures by molecular mechanics and molecular dynamics.
• Protein-Ligand docking - Drug design
• Protein-protein structural recognition (docking)
• Structure quality evaluation methods - Methods for stereochemical structure checks

Coordinator: Prof. S. Hamodrakas

Lecturers: Prof. S. Hamodrakas

PART I The JAVA programming language

• Classes and Objects, Java foundation classes, Applets and Applications, Topics in Graphical User Interface design, Distributed computing, JavaBeans, JAVA applications in Bioinformatics - the BIOJAVA project

PART II The perl programming language

• Scalar variables, lists, arrays, strings. Flow control structures. Subroutines, Associative arrays (hashes). Input/output. Pattern matching with regular expressions. Perl applications in Bioinformatics - the BIOPERL project.

Coordinator: Prof. I. Iliopoulos

Lecturers: Prof. S. Hamodrakas | Prof. E. Iliopoulos | Dr. M Vlasi | Dr. V. Oikonomidou

• Structural elements of biomolecules: Size and environment of biomolecules
• Biomolecular interactions: Protein-protein interaction types, Protein-DNA interaction types
• Molecular recognition: Binding and dissociation constants, Binding energy, A molecular recognition example, Entropy terms in complex creation, Degrees of molecular recognition - high fidelity recognition, Evolution and molecular recognition, Interactions of proteins and nucleic acids.
• Energetic analysis of interactions: Molecular mechanics, Introduction to the methodology of "ab initio" protein folding, the empirical function of energy, energy minimization, energy surface, Enthalpy and entropy, Molecular dynamics.
• Protein folding - molecular chaperones: New approaches for protein folding with or without intermediate states, The value of molecular topology, Molecular chaperones.
• Biological membranes and membrane proteins: Composition and structure of biological membranes, membrane proteins, Membrane protein structure, Families of membrane proteins, Channels and receptors.
• Cellular Translocation of proteins: The endoplasmic reticulum function, protein targeting and signal sequences, protein translocation in mitochondria, chloroplasts and the nucleus.
• Drug design: Methodology, Drug design based on target?s structure, Problems - Resistance of infectious diseases and cancer against therapeutic agents.
• Chemical signal transduction: Usual molecular mechanisms for signal transduction, Hormones, Neurotransmitters, Signal transduction in membranes and cytoplasm, Steroid hormones and their receptors. Feromones.

Coordinator: Prof. S. Hamodrakas

Lecturers: Prof. S. Hamodrakas | Prof. L. Margaritis | Prof. E. Moudrianakis | Assoc. Prof. G. Rodakis | Prof. E. Iliopoulos | Lecturer G. Goulielmos

• General issues
• Science, Scientific Field and Scientific Research
• Biological research.
• Ethics in scientific research and specifically in biological sciences
• Bioinformatics and moral dilemmas. The role of a bioinformatician in different stages of a project.
• Writing, evaluating and publishing the results of scientific research in the academic press (journals, conferences etc).
• Choosing the appropriate journal (Sources, Information, Instructions to authors, peer review system, journal evaluation)
• Type of Articles (review, letters etc). Scientific paper format (Abstract, Introduction, Materials and Methods, Results, Discussion).
• Assessment of a submitted paper through the peer review system. Answering reviewer?s comments.
• Applications.