protein secondary structure prediction methods tdveaavnslvnlylqasyls “from sequence to...

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

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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 predict aspects of protein structure and function

Page 3: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

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…

Secondary Structure prediction:

Query

SwissProt

BLASTp

QuerySubjectSubjectSubjectSubject

psiBLAST,MaxHom MSA

Machine LearningApproach

HHHLLLHHHEEE

Known structures

Page 5: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

PROFsec and PSIpred

Two secondary structure prediction tools:

• PROFsec– Based on sequence family alignments (MAXHOM)

• PSIpred– Based on PSI-BLAST profiles

Page 6: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

http://www.predictprotein.org/main.php

Page 7: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

input

output

Page 8: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

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.

Page 9: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

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.

Page 10: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

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1 2

OUTPUT

Page 12: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

HelixLoop

Beta

HelixLoop

Beta

Page 13: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

PSIpred

Input sequence

Type of Analysis(PSIPRED,MEMSAT,

genTHREAD)

http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

Page 14: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

PSIpredFiltering Options

Email address

GO!

Page 15: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

PSIPRED secondary structure prediction

Page 16: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

PROFsec PSIpred

Page 17: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

TMHMM – transmembrane domain prediction

http://www.cbs.dtu.dk/services/TMHMM/

Page 18: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

Page 19: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

Predict Start End

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Sequence and SecondaryStructure

information

Page 22: Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to structure”

Sequence DetailsTurn Helix

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protein secondary structure prediction methods tdveaavnslvnlylqasyls “from sequence to...

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structure slide

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protein structure prediction

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kind of prediction