EMBO Practical Course - Protein Bioinformatics Tools- Focus on Regulatory Proteins: Sequences, Struc

Venue: EMBL Advanced Training Centre

Location: 60117 Heidelberg, Germany

Event Date/Time: Sep 25, 2011 End Date/Time: Oct 01, 2011
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In recent years it has become apparent that structure-function relationships of proteins, particularly cellular regulatory proteins, are much more complex than had been anticipated. This is causing difficulties for researchers as they try to move beyond overly simplified models of regulatory systems throughout the cell. It is critical that they learn to appreciate, analyse, and characterise the modular complexity of the proteins they study; understanding protein function is central to analysis of any cellular system, and protein modular architecture specifies protein function, Protein modules (e.g. globular domains, coiled-coil regions, linear motifs), their structure, diversity, interactions, and direct experience using bioinformatic tools for characterising and predicting them, are the principal themes of the course - explored with a focus on cell regulatory proteins, which display exceptional modular diversity. In particular, in this course we will highlight the importance of intrinsically disordered protein (IDP) modules- given the burgeoning awareness of the key roles they play in diverse cellular systems, especially in regulation and signaling.

The principal objective is to improve the ability of the participants to use bioinformatics tools to analyse and predict modular protein architecture - while additionally improving their understanding of module diversity and the theoretical basis of analysis methods. This will improve the participants' ability to critically interpret and apply relevant techniques to their studies and those of others. Additionally, we aim to raise awareness of several fundamental bioinformatics concepts and ideas important for understanding more specialised tools and applications, while providing direct experience using key software including SMART, CLUSTALX, BLAST, JalView, PFAM, ELM, STRING, REFLECT, IUPRED, PhosphoELM and others. This will help participants to transfer what they learn during the course back to their own labs. We will also enable direct personal access to developers of several commonly used tools - providing definitive advice on problems and questions the students may have understanding and using the software, while facilitating future contacts between teachers and participants.

Practical sessions during the course will focus on developing the student’s familiarity and expertise in using the most commonly used software tools for analysis of protein modular architecture. The developers of several of these packages will be attending the meeting (Alex Bateman - PFAM; Toby Gibson - ELM, CLUSTALX, Zsuzsanna Dosztanyi and Peter Tompa: IUPRED; Michael Yaffe: ScanSite; Francesca Diella: PhosphoELM; Lars Juhl Jensen: STRING, STITCH, REFLECT). Thus, students will have the opportunities to address any questions they may have concerning these software directly to the developers.

Additionally, practicals will focus on developing the participants understanding of several key concepts including: statistics of sequence similarity search tools; approaches to text-based database-searches; interpretation of sequence alignments; protein 3D structure. Other practical sessions (those on the first day) will focus on familiarizing the participants with the computational environment provided on the teaching machines (which will be running LINUX).

The participants are expected to present a poster of their work. The posters will be available for viewing throughout the entire meeting. More details about the poster presentation will be given to the selected participants.


Meyerhofstr. 1