protein secondary structure prediction methods
DESCRIPTION
Protein secondary structure prediction methods. “From sequence to structure”. TDVEAAVNSLVNLYLQASYLS. What are they? Sequence-based tools for protein structure prediction. What do they do? they Search for similar protein sequences in a database. - PowerPoint PPT PresentationTRANSCRIPT
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Protein secondary structure prediction methods
TDVEAAVNSLVNLYLQASYLS
“From sequence to structure”
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• 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
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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…
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Secondary Structure prediction:
Query
SwissProt
BLASTp
QuerySubjectSubjectSubjectSubject
psiBLAST,MaxHom MSA
Machine LearningApproach
HHHLLLHHHEEE
Known structures
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PROFsec and PSIpred
Two secondary structure prediction tools:
• PROFsec– Based on sequence family alignments (MAXHOM)
• PSIpred– Based on PSI-BLAST profiles
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http://www.predictprotein.org/
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Input
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Output
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PSIpred
Input sequence
Type of Analysis(PSIPRED,MEMSAT,
genTHREAD)
http://bioinf.cs.ucl.ac.uk/software_downloads/
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http://bioinf.cs.ucl.ac.uk/web_servers/
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PSIPRED secondary structure prediction
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PROFsec PSIpred
?
?
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TMHMM – transmembrane domain prediction
http://www.cbs.dtu.dk/services/TMHMM/
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Predict Start End
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Sequence and SecondaryStructure
information
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Sequence DetailsTurn Helix
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Excersize The sequence below belongs to the Prion that causes the “mad cow” disease. This protein becomes toxic
when it gets into the brain and misfolds causing native cellular prions to deform and aggregate. In structural terms, the prion toxicity in leaded by a folding change into an instable structure.
>PRION_1ag2
GLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY
1. Use Predict Protein (PROFsec) to predict its secondary structures.
2. What is the secondary structure in the real solved structure based on the PDB?
3. Given the prediction results and the secondary structure of the real solved structure can you suggest the region which could be responsible for the structural instability?
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1. Predict Protein (PROFsec)
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2. PDB (DSSP)
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3. Answer : alpha helix PDB (DSSP)turn into B-sheet Predict Protein (ROFsec),
prediction in this area are not consistent.