Student-Faculty Programs Office
Summer 2017 Announcements of Opportunity

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Project:  Structural and Functional Bioinformatics Toolbox for G Protein Coupled Receptors
Disciplines:  Multidisciplinary, Bioinformatics and Computer Science
Mentor:  Ravi Abrol, Visiting Scientist, (CCE), abrol@caltech.edu, Phone: 626-320-4987
Mentor URL:  http://www.csun.edu/science-mathematics/chemistry-biochemistry/ravinder-abrol  (opens in new window)
AO Contact:  Ravi Abrol, abrol@caltech.edu
Background:  G protein coupled receptors (GPCRs) are integral membrane
proteins that enable cells to convert extracellular signals
into intracellular and physiological responses. This has
made them targets of ~40% of the drugs in the clinic. The
current golden era of GPCR biology is being catalyzed by
major advances in their structural and functional biology.
This is greatly expanding our knowledge about how these
receptors work, which is opening opportunities for
combining this structural and functional knowledge with
their evolutionary and sequence information for an
integrative study of GPCRs. This will enable the generation
of new hypotheses and will open new lines of investigation into the functioning of these vital receptors.
Description:  We are developing an integrative knowledge-base on GPCRs that
will be useful for both teaching and research and is
bringing together their sequence, structure, signaling,
mutation, and disease-link knowledge.

As part of this project, the student will develop a toolbox
of structural bioinformatics methods that will enable an
efficient interface to the GPCR knowledge-base. This will
allow potential users of the knowledge-base to setup
customized searches based on sequence motifs, structural
signatures, ligand binding, mutations, signaling
pathways, and disease associations. This toolbox will be
deployed at www.gpcrkb.org.

The student will write scripts to interface with existing
bioinformatics, structural/pharmacological databases, and
our internal GPCR database. These scripts will be integrated
into the web interface at gpcrkb.org along with the ability
to run customized searches around specific GPCRs or using
sequence, structure, mutation, and functional information.
References:  1. http://www.guidetopharmacology.org/GRAC/ReceptorFamiliesForward?type=GPCR
2. http://www.gpcrs.org
3. Cvicek et al. PLoS Comput Biol. 2016 Mar 30;12(3):e1004805. doi: 10.1371/journal.pcbi.1004805
Student Requirements:  The ideal student will have a strong interest in Programming
and Biology. Should be proficient in Python or Perl and have
a working knowledge of MySQL. Reading in Bioinformatics will
be provided after SURF acceptance.
This project is based at California State university
Northridge, where daily carpool option is available with
the Mentor during the SURF.
Programs:  This AO can be done under the following programs:

  Program    Available To
       SURF    Caltech students only 

Click on a program name for program info and application requirements.


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Problems with or questions about submitting an AO?  Call Jen Manglos of the Student-Faculty Programs Office at (626) 395-2885.
 
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