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Protein secondary structure prediction methods

Protein secondary structure prediction methods. “From sequence to structure”. TDVEAAVNSLVNLYLQASYLS. What are they? Sequence-based tools for protein structure prediction. What do they do? they Search for similar protein sequences in a database.

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Protein secondary structure prediction methods

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  1. Protein secondary structure prediction methods “From sequence to structure” TDVEAAVNSLVNLYLQASYLS

  2. What are they? • Sequence-based tools for protein structure prediction. • What do they do? • they Search for similar protein sequences in a database. • Based on the similarity to these sequences they predict aspects of protein structure and function

  3. What kind of prediction can we perform? • Secondary Structure: Helix, Strands, Loops (PHDsec,PSIPRED). • Predicts transmembrane helices (PHDhtm,MEMSAT,TMHMM). • Fold structure (genTHREADER). • Solvent accessibility: important for the prediction of ligand binding sites (PHDacc). • Other features: Coiled Coils, Globular regions, Disulfide Bonds and more…

  4. Secondary Structure prediction: HHHLLLHHHEEE Query BLASTp SwissProt Machine Learning Approach psiBLAST, MaxHom Known structures MSA Query Subject Subject Subject Subject

  5. PROFsec and PSIpred • Two secondary structure prediction tools: • PROFsec • Based on sequence family alignments (MAXHOM) • PSIpred • Based on PSI-BLAST profiles

  6. http://www.predictprotein.org/

  7. Input

  8. Output

  9. http://bioinf.cs.ucl.ac.uk/software_downloads/ PSIpred Input sequence Type of Analysis (PSIPRED,MEMSAT, genTHREAD)

  10. http://bioinf.cs.ucl.ac.uk/web_servers/

  11. PSIPRED secondary structure prediction

  12. PROFsec PSIpred ? ?

  13. TMHMM – transmembrane domain prediction http://www.cbs.dtu.dk/services/TMHMM/

  14. Start End Predict

  15. Sequence and Secondary Structure information

  16. Sequence Details Turn Helix

  17. Excersize The sequence below belongs to the Prion that causes the “mad cow” disease. This protein becomes toxic when it gets into the brain and misfolds causing native cellular prions to deform and aggregate. In structural terms, the prion toxicity in leaded by a folding change into an instable structure. >PRION_1ag2 GLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY • Use Predict Protein (PROFsec) to predict its secondary structures. • What is the secondary structure in the real solved structure based on the PDB? • Given the prediction results and the secondary structure of the real solved structure can you suggest the region which could be responsible for the structural instability?  

  18. 1. Predict Protein (PROFsec)

  19. 2. PDB (DSSP)

  20. 3. Answer : alpha helix PDB (DSSP)turn into B-sheet Predict Protein (ROFsec), prediction in this area are not consistent.

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