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SUMMARY:Learning spatial amino acid contacts from many homologous protein 
 sequences
DTSTART:20130226T161500
DTEND:20130226T171500
DTSTAMP:20260510T235040Z
UID:28b2897953f2d37ce32f41957082a4739cfe4c5bbf27296f0817bfa8
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Erik Aurell\, KTH Stockholm\nSpatially proximate amino a
 cids in a protein can be asumed to co-evolve and a protein's three-dimensi
 onal (3D) structure hence\nleave an echo of correlations in the evolutiona
 ry record. Reverse engineering 3D structures from such correlations would 
 be\nimportant in  biology\, as the number of known protein sequences is m
 uch larger and grows much faster than the number\nof known protein structu
 res. Within this task lies a statistical inference problem\, rooted in the
  following: correlation between two\nsites in a protein sequence can arise
  from firsthand interaction but can also be network-propagated via interme
 diate sites\; observed\ncorrelation is not enough to guarantee proximity.\
 nAn approach to separating direct from indirect interactions is to learn a
  plausible probabilistic model from the data\, and then score putative int
 eractions by the corresponding terms in the model. In the context of prote
 in sequences and learning the a model of at most pair-wise interactions (a
  Potts model) this approach has been referred to as direct-coupling analys
 is.\nThe computational tasks involved are not trivial as in these problems
  a maximum likelihood approach is unfeasible\, and one must resort to appr
 oximations.\nI will discuss this field focusing on our recent result that 
 the pseudolikelihood method somewhat outperforms other approaches to the d
 irect-coupling analysis.\nThis is joint work with Magnus Ekeberg\, Cecilia
  Lövkvist\, Yueheng Lan and Martin Weigt published in Phys. Rev. E 87\, 0
 12707 (2013)\, URL:        http://link.aps.org/doi/10.1103/PhysRevE
 .87.012707\nCode implementing the pseudolikelihood method for these proble
 ms is available at http://plmdca.csc.kth.se/.
LOCATION:INR113 http://plan.epfl.ch/?lang=fr&room=inr113
STATUS:CONFIRMED
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