Team MODBIO

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Section: New Results

Keywords : Statistical learning, protein secondary and tertiary structure, kernel engineering, disulphide bridges.

Protein structure prediction

Participants : Yannick Darcy, Yann Guermeur, Frédéric Sur.

Knowing the three-dimensional structure of a protein can greatly help to infer its function. Predicting this tertiary structure from the sequence of amino acids (or primary structure ), remains one of the central open problems in structural biology. This is the subject of the «GENOTO3D» project that we coordinate. This year, our main efforts have been concentrated on the development of a new kernel for our M-SVM dedicated to protein secondary structure prediction, a kernel based on a pair-HMM.

Our collaboration with Nicolas Sapay and Gilbert Deléage, at IBCP, in Lyon, on the prediction of amphipathic in-plane membrane anchors in motopic proteins, has given birth to a new prediction method, «AmphipaSeek»  [29] , which is available from the website of the PBIL, at the following address : http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_amphipaseek.html .


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