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Phyre2. Dr. Lawrence Kelley Structural Bioinformatics Group Imperial College London. Phyre2. SVYDAAAQLTADVKKDLRDSW KVIGSDKKGNGVALMTTLFAD NQETIGYFKRLGNVSQGMAND KLRGHSITLMYALQNFIDQLD NPDSLDLVCS ……. Predict the 3D structure adopted by a user-supplied protein sequence.

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phyre2

Phyre2

Dr. Lawrence Kelley

Structural Bioinformatics Group

Imperial College London

slide2
Phyre2

SVYDAAAQLTADVKKDLRDSW

KVIGSDKKGNGVALMTTLFAD

NQETIGYFKRLGNVSQGMAND

KLRGHSITLMYALQNFIDQLD

NPDSLDLVCS…….

Predict the 3D structure adopted by a user-supplied protein sequence

slide5
Phyre2

Homologous sequences

ARDLVIPMIYCGHGY

User sequence

Search the 10 million known sequences for homologues using PSI-Blast.

slide6
Phyre2

HMM

ARDLVIPMIYCGHGY

User sequence

PSI-Blast

Hidden Markov model

Capture the mutational propensities at each position in the protein

An evolutionary fingerprint

slide7
Phyre2

~ 65,000 known 3D structures

slide8
Phyre2

~ 65,000 known 3D structures

slide9
Phyre2

Extract sequence

HAPTLVRDC…….

~ 65,000 known 3D structures

slide10
Phyre2

Extract sequence

HAPTLVRDC…….

~ 65,000 known 3D structures

PSI-Blast

slide11
Phyre2

Extract sequence

HAPTLVRDC…….

~ 65,000 known 3D structures

PSI-Blast

HMM

Hidden Markov model

for sequence of KNOWN structure

slide12
Phyre2

HMM

HMM

HMM

~ 65,000 known 3D structures

~ 65,000 hidden Markov models

slide13
Phyre2

Hidden Markov Model Database of

KNOWN

STRUCTURES

~ 65,000 known 3D structures

slide14
Phyre2

HMM

ARDLVIPMIYCGHGY

PSI-Blast

Hidden Markov model

Capture the mutational propensities at each position in the protein

An evolutionary fingerprint

slide15
Phyre2

HMM

ARDLVIPMIYCGHGY

PSI-Blast

Hidden Markov Model DB of KNOWN

STRUCTURES

HMM-HMM

matching

Alignments of user sequence to known structures

ranked by confidence.

ARDL--VIPMIYCGHGY

AFDLCDLIPV--CGMAY

Sequence of known structure

slide16
Phyre2

HMM

ARDLVIPMIYCGHGY

PSI-Blast

Hidden Markov Model DB of KNOWN

STRUCTURES

HMM-HMM

matching

ARDL--VIPMIYCGHGY

AFDLCDLIPV--CGMAY

3D-Model

Sequence of known structure

slide17
Phyre2

HMM

ARDLVIPMIYCGHGY

PSI-Blast

Hidden Markov Model DB of KNOWN

STRUCTURES

Very powerful –

able to reliably detect extremely

remote homology

HMM-HMM

matching

Routinely creates accurate models even

whensequence identity is <15%

ARDL--VIPMIYCGHGY

AFDLCDLIPV--CGMAY

3D-Model

Sequence of known structure

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