Monday, 10 September 2012

ECCB'12: Tutorial on Protein evolution

During the ECCB'12 conference in Basel, Switzerland, I had the opportunity to organise and present a tutorial entitled "Protein Evolution: From Sequence to Structure to Function", along with Christine Orengo (UCL) and Nicholas Furnham (EMBL-EBI). This tutorial attracted 44 participants.

In the morning session, the participants were introduced to various softwares to identify functional shift in multiple alignments of protein sequences. These sofwares included BADASP, TDG09, FunDi and Diverge2. Jalview and PyMol were used to visualise the results.
They also used CodeML from the PAML package to inference positive selection during the evolution of nucleotide coding sequences. CodeML contains various codon substitution models that estimate different dN/dS. In particular the branch-site model was described in details.

The tutorial of this section is available here:
http://www.cathdb.info/wiki/doku.php?id=tutorials:eccb_t2_studer


In the afternoon, Christine Orengo presented the fundamental concept of CATH. CATH is database of domain superfamilies initially identified using structural data and then expanded with predicted domain structures in genome sequences. Structural similarities are identified using the CATHEDRAL algorithm (Redfern, Orengo, 2007) and homologous relationships are then confirmed using sequence based HMM-HMM approaches (eg HHpred, Hildebrand 2009). CATH superfamilies are now also subclassified into functional families (FunFams) and new pages presenting these families and
conserved residues identified and projected onto representative structures were demoed during the session.


During the practical, Ian Sillitoe, one of the main CATH computational scientists, presented the new release of the CATH database.

The tutorial of this section is available here:
http://www.cathdb.info/wiki-readonly/doku.php?id=tutorials:workshop


Finally, Nick Furnham presented FunTree, a new resource, developed in the laboratory of Prof. Janet Thornton at the European Bioinformatics Institute, in collaboration with Prof. Christine Orengo at UCL. It brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies.
During the practical, he showed how the wide variety of data captured in FunTree from CATH/CATH-Gene3D, PDB, UniProtKB, ArchSchema, CSA, MACiE, ChEBI and KEGG is gathered, analysed and displayed.

The tutorial of this section is available here:
http://www.ebi.ac.uk/thornton-srv/databases/FunTree/templates/ECCB12Tutorial.php

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