"" " As a result of attending the course, trainees should be better able to:
- Identify previously-reported data on PPIs from databases
- Use bioinformatics tools to predict protein modules from protein sequences
- Visualise and analyse data on the 3D structure of PPIs, and of PPI networks
- Describe ways in which PPIs have been targeted, using bioinformatics approaches, in drug design
- Describe the characteristics of PPIs mediated between different kinds of protein modules
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Tools used and practical exercises taught will focus on the following use-cases:
- retrieving previously-reported PPI data associated with protein(s) of interest (and other kinds of data), using resources such as UniProt, IntAct, MINT, ePDB/PDB, PhosphoELM, REFLECT, and others
- predicting protein interaction modules from protein sequence, using resources such as PFAM, SMART, InterPro, ELM, IUPRED, ScanSite, and others
- identifying modules in PPI networks, and predicting their function, using resources such as STRING, STITCH, and Cytoscape
- identifying residues likely to be involved in direct physical contact between proteins in PPIs, using resources such as CLUSTALX, JalView, PyMOL, and PISA
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Additionally, practicals will focus on developing the participants' understanding of several key concepts including: interpretation of sequence alignments; concepts associated with protein 3D structure; the structural diversity of PPIs; and structures of biological databases.
In several cases, developers of the packages used during the course are trainers in the course (Toby Gibson, ELM, CLUSTALX; Zsuzsanna Dosztanyi, IUPRED; Michael Yaffe; ScanSite; Francesca Diella: PhosphoELM, ELM; Lars Juhl Jensen: STRING, STITCH, REFLECT; Gary Bader and Piet Molenaar, Cytoscape). " ""
EMBO 2012 PRACTICAL COURSE INFORMATION & REGISTRATION
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"Nanotechnology for the biologist"
Journal of Leukocyte Biology vol. 78 no. 3 585-594
September 2005
http://www.jleukbio.org/content/78/3/585.full
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