Tag: bachelor projects

The influence of protein dynamics on structural alignments

The influence of protein dynamics on structural alignments

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Minor project at the The Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands. Under supervision of Prof Heringa, Dr. Feenstra and Dr. Pirovano.

Current structural alignment methods don’t consider structural variance. By modelling protein dynamics on HOMSTRAD homologous proteins (with GROMACS) a new set of structural variant protein structures was created that respond to different “normal” stages of a protein structure. Dalilite structural alignments were made made and scored using sum-of-pairs. By comparing the sum-of-pairs score obtained with Dalilite and the RMSD divergence scores from our simulations we gained insight in how well structural alignment tools can deal with different sort of normal structural variance.

Part of my work has been published in the following publication: The meaning of alignment: lessons from structural diversity

THINGS – THis Is Not GeneSeeker

THINGS – THis Is Not GeneSeeker

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Bachelor internship at:

Under supervision of Prof Leunissen (WUR), Herman van den Berg (Vertis) and  Koen Cuelenaere (Dalicon).

Creating a Oracle RDF based Pubmed text mining for finding relations between “health” related MESH terms and food items by using genes.

Most of the work consisted of working with the latest Oracle 10g2 techniques that implemented the first version of a RDF based database. Using a RDF database you can input all your data in your database and only define the structure (as what you would normally do in a relational database like MySQL). This way the database can quickly find new ways of overlap between data over multiple layers of information (as in this kind of database there is no root nor leafs all data can be related and queried this way).

 

Peritonitis in CAPD patients – a proteomics analysis

Peritonitis in CAPD patients – a proteomics analysis

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Bachelor thesis at  Nijmegen Proteomics Facility, Laboratorium voor Kindergeneeskunde en Neurologie, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands. Under supervision of Dr L. van den Heuvel and W. Pluk.

Built a central web-based data storage for proteomics data that can handle first steps of analysis automatically. Normalisation, ratio conversation, emPAI calculations and mapping found proteins/peptides onto KEGG and GO ontologies for a global overview of sample content.

System was then used for a research project where several samples of CAPD patients with and without peritonitis where analysed and where compared on protein abundance. There was not enough statistical power in our 13 samples to identify peritonitis specific proteins or peptides as the normal experimental and biological noise was bigger than the intra-individual signals.