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

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Presentation transcript:

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

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

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…

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

PROF sec and PSIpred Two secondary structure prediction tools: PROFsec –Based on sequence family alignments (MAXHOM) PSIpred –Based on PSI-BLAST profiles

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.

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.

OUTPUT

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

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 = %. Rel_acc:Reliability of prediction. SUB_acc:Subset of predictions with high reliability. H= Helix, E=Sheet, L=loop

PSIpred Input sequence Type of Analysis (PSIPRED,MEMSAT, genTHREAD)

PSIpred Filtering Options address GO!

PSIPRED secondary structure prediction

PROFsecPSIpred ? ?

TMHMM – transmembrane domain prediction

Predict StartEnd

ferritin

Java based visualization tools PDB file Accession number General Info

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

Experimental Description. i.e. crystallography info.

Structure classification

Sequence and Secondary Structure information

Sequence Details TurnHelix