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

2. What are they? –Sequence-based tools for protein structure prediction. What do they do? 1.they Search for similar protein sequences in a database. 2.Based on the similarity to these sequences they predict aspects of protein structure and function

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

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

5. PROF sec 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/main.php

7. input output

8. PROFsec:Profile-based neural network prediction of secondary structures. ASP:Predicts conformational switches (e.g from α-helix to β-sheet. ProSite:Scan Prosite for functional motifs. PredictNLS:Predicts nuclear localization based on known data.

9. DISULFIND:Find disulfide bonds. ProDom:Search database of putative domains. PROFacc:Predict Solvent Accessibility COLIS:Predict coiled-coil structures SEG:Sequence Complexity PHDhtm:Transmembrane domains.

11. 12 OUTPUT

12. 1 2 Helix Loop Beta Helix Loop Beta L H E

13. PSIpred Input sequence Type of Analysis (PSIPRED,MEMSAT, genTHREAD) http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

14. PSIpred Filtering Options Email address GO!

15. PSIPRED secondary structure prediction

16. PROFsecPSIpred ? ?

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

19. Predict StartEnd

21. Sequence and Secondary Structure information

22. Sequence Details TurnHelix