Predicting protein folding

Team Prion

IRC channel

Project Proposal Phase

• Project Proposal (doc) (pdf)
• Milestone 1 Report (see e-mail)
• Milestone 2 Report (see e-mail)

Background information on Wikipedia

• (α)Amino Acid*New*
  • amino acid residue(R), Amine and Carboxyl linked at α-carbon
  • A Protien is a string amino acid residues held together by Peptide Bonds
  • The amino acid residue sequence is the primary protein structure
• Peptide Bond *New*
• Standard Amino Acids and Abbreviations *New*
• Protein structure prediction
• Homology modelling
• Secondary Structure
  • Talks about the prediction accuracy in the past using a DSSP model (<=~80%)

Useful links

• Submitting to NCBI BLAST server
• NCBI BLAST Java Interface
• Bioinformatics Wiki
• PDB File Format (1996)
• Jim Davies, Janice Glasgow, Tony Kuo: Visio-spatial Case-Based Reasoning: A Case Study in Prediction of Protein Structure
• EVA Competition
• STRIDE tertiary to secondary
• DSSP Program and May-2007 DB
• Use Above - EVA DSSP Database
• UGA BioInfo BLAST
• Java+XML Tutorial

Todo

• Evaluate our reuse method

Sequence Similarity references

Papers

• Optimization Approaches to Protein Folding
• http://cssb.biology.gatech.edu/skolnick/publications/pdffiles/224.pdf