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SUMMARY:Domain swapping in proteins - Dr Sowdhamini\, National Centre for 
 Biological Sciences (TIFR) UAS-GKVK Campus Bellary Road Bangalore 560 065 
 INDIA
DTSTART:20111221T101500Z
DTEND:20111221T111500Z
UID:TALK34632@talks.cam.ac.uk
CONTACT:23791
DESCRIPTION:Structures of protein domains offer a dataset to understand th
 e features that mediate their biological function. 3D domain swapping is a
  structural phenomenon observed in a variety of proteins as a mechanism fo
 r dimer or higher oligomeric formation. It is also implicated in neurodege
 nerative diseases since domain swapping could mediate unlimited oligomeris
 ation. Data on all the available protein structural entries involved in th
 is mechanism have been curated. Information on domain swapping has been ob
 tained from the literature and bioinformatics tools and database resources
  and reported in a new database\, “3Dswap”\, for 293 non-redundant pro
 tein structures. We propose a quantitative method ‘extent of swapping’
  to classify proteins involved in swapping mechanism and observed that lar
 ge amount of proteins belong to the class of “moderately swapped” prot
 eins. Structural entries from 3DSwap contribute to the ‘positive dataset
 ’ and used for the development of machine learning-based approaches for 
 the identification of sequence and structural features mediating 3D domain
  swapping. Support Vector Machine (SVM) and Random Forest (RF) based algor
 ithms were developed to predict swapping from structure and mere sequence 
 information. These prediction methods achieve 73% and 64% accuracy\, respe
 ctively. I will also describe some structural analyses associated with the
 se studies.  
LOCATION:Perham's seminar room
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