Protein secondary structure prediction methods TDVEAAVNSLVNLYLQASYLS “From sequence to...
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Transcript of 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