Mining Protein Structure Data
José Carlos Almeida Santos,
Imperial College London –
This presentation will show the application of data mining techniques, in particular of machine learning, for discovery of knowledge in a protein database.
The main problem we address is the determination whether an amino acid is exposed or buried in a protein for five exposition levels: 2%, 10%, 20%, 25% and 30%.
First we introduce the baseline classifier for this problem which, although very simple (only takes into account the amino acid type), already achieves good prediction results. Then we explain how, by making a local PDB database, retrieving DSSP and SCOP data, we build our classifier to improve the baseline prediction.
Finally we test and compare several classifiers (Neural Networks, C5.0, CART and Chaid), and parameters that might influence the prediction accuracy. Namely the level of information per amino acid, the SCOP class of the protein and the neighbourhood of the current amino acid (i.e.: the sliding window size).
Keywords: Amino acid Relative Solvent Accessibility, Protein Structure
Prediction, Data Mining, BioInformatics, Artificial Intelligence
Date: 2007-Feb-01 Time: 16:00:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.