GSoC2011 mtrellet

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Revision as of 18:51, 23 May 2011

Contents

Author & Mentors

Mikael Trellet mikael.trellet@gmail.com

Mentors

Joao Rodrigues
Eric Talevich


Abstract

Analysis of protein-protein complexes interfaces at a residue level yields significant information on the overall binding process. Such information can be broadly used for example in binding affinity studies, interface design, and enzymology. To tap into it, there is a need for tools that systematically and automatically analyze protein structures, or that provide means to this end. Protorop (http://www.bioinformatics.sussex.ac.uk/protorp/) is an example of such a tool and the elevated number of citations the server has had since its publication acknowledge its importance. However, being a webserver, Protorop is not suited for large-scale analysis and it leaves the community dependent on its maintainers to keep the service available. On the other hand, Biopython’s structural biology module, Bio.PDB, provides the ideal parsing machinery and programmatic structures for the development of an offline, open-source library for interface analysis. Such a library could be easily used in large-scale analysis of protein-protein interfaces, for example in the CAPRI experiment evaluation or in benchmark statistics. It would be also reasonable, if time permits, to extend this module to deal with protein-DNA or protein-RNA complexes, as Biopython supports nucleic acids already.


Project Schedule

Week 1 [23rd May - 31st June]

Add the new module backbone in current Bio.PDB code base

  • Evaluate possible code reuse and call it into the new module
  • Try simple calculations to be sure that there is stability between the different modules (parsing for example) and functions


Define a stable benchmark

  • Select few PDB files among interface size and proteins size would be different
  • Add some basics unit tests


Weeks 2-3 [1st - 13th June]

Extend IUPAC.Data module with residue information

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