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 predicts 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/newwebsite/submit.php

7. 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.

8. 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.

9. OUTPUT

11. number of aligned sequences in HSSP file (Homology derived Secondary Structure)

12. OBS_sec: Observed secondary structures (if any). PROF_sec:Predicted secondary structures. Rel_sec:Reliability of the prediction. SUB_sec:Subset of predictions with high reliability. O_3_sec:Observed surface accessibility. P_3_sec:Predicted surface accessibility. b = 0-9%, i = 9-36%, e = 36-100%. Rel_acc:Reliability of prediction. SUB_acc:Subset of predictions with high reliability. H= Helix, E=Sheet, L=loop

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

16. PSIpred Filtering Options Email address GO!

17. PSIPRED secondary structure prediction

18. PROFsecPSIpred ? ?

19. TMHMM – transmembrane domain prediction

21. Predict StartEnd

22. ferritin

25. Java based visualization tools PDB file Accession number General Info

26. PDB provides the atomic coordinates of the structure : Which can be viewed by different visualization tools

27. Experimental Description. i.e. crystallography info.

28. Structure classification

29. Sequence and Secondary Structure information

30. Sequence Details TurnHelix

31. http://www.ebi.ac.uk/pdbsum/