Research Projects

Ideas for original research projects, as opposed to simply software.

Membrane protein loops: modelling and docking

Aims

1. Obtain protein sequences (fasta) from complete genomes of "medically-relevant" organisms
2. Predict external (outside) transmembrane protein loop regions (TMHMM?)
3. Get best templates for modelling (BLAST nr PDB set or use modeller align script to pdb95_pir)
4. Model using (Prospect2?) + MODELLER? pipeline
5. Screen for binding to some diversity set using AutoDock
6. Database + web frontend to all data

Started this in Perl (Trac project), but better in Ruby or other.

Prokaryotic genomes: database + analysis of intergenic regions

• First step: implement (bio)ruby code to extract intergenic regions from (GenBank?) sequence