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

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

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

PROFsec and PSIpred

Two secondary structure prediction tools:

• PROFsec– Based on sequence family alignments (MAXHOM)

• PSIpred– Based on PSI-BLAST profiles

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

input

output

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.

1 2

OUTPUT

1

2

HelixLoop

Beta

HelixLoop

Beta

LH

E

PSIpred

Input sequence

Type of Analysis(PSIPRED,MEMSAT,

genTHREAD)

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

PSIpredFiltering Options

Email address

GO!

PSIPRED secondary structure prediction

PROFsec PSIpred

?

?

TMHMM – transmembrane domain prediction

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

Predict Start End

Sequence and SecondaryStructure

information

Sequence DetailsTurn Helix