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Phyre2 Dr. Lawrence Kelley Structural Bioinformatics Group Imperial College London.

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Presentation on theme: "Phyre2 Dr. Lawrence Kelley Structural Bioinformatics Group Imperial College London."— Presentation transcript:

1 Phyre2 Dr. Lawrence Kelley Structural Bioinformatics Group Imperial College London

2 SVYDAAAQLTADVKKDLRDSW KVIGSDKKGNGVALMTTLFAD NQETIGYFKRLGNVSQGMAND KLRGHSITLMYALQNFIDQLD NPDSLDLVCS……. Predict the 3D structure adopted by a user-supplied protein sequence Phyre2

3

4 How does Phyre2 work?

5 ARDLVIPMIYCGHGY Search the 10 million known sequences for homologues using PSI-Blast. Phyre2 Homologous sequences User sequence

6 ARDLVIPMIYCGHGY HMM PSI-Blast Phyre2 Hidden Markov model Capture the mutational propensities at each position in the protein An evolutionary fingerprint User sequence

7 ~ 65,000 known 3D structures Phyre2

8 ~ 65,000 known 3D structures Phyre2

9 ~ 65,000 known 3D structures Phyre2 HAPTLVRDC……. Extract sequence

10 ~ 65,000 known 3D structures Phyre2 HAPTLVRDC……. PSI-Blast Extract sequence

11 ~ 65,000 known 3D structures Phyre2 HAPTLVRDC……. HMM PSI-Blast Hidden Markov model for sequence of KNOWN structure Extract sequence

12 ~ 65,000 known 3D structures Phyre2 HMM ~ 65,000 hidden Markov models

13 ~ 65,000 known 3D structures Phyre2 Hidden Markov Model Database of KNOWN STRUCTURES Hidden Markov Model Database of KNOWN STRUCTURES

14 ARDLVIPMIYCGHGY HMM PSI-Blast Phyre2 Hidden Markov model Capture the mutational propensities at each position in the protein An evolutionary fingerprint

15 ARDLVIPMIYCGHGY HMM PSI-Blast Hidden Markov Model DB of KNOWN STRUCTURES Hidden Markov Model DB of KNOWN STRUCTURES HMM-HMM matching Phyre2 Alignments of user sequence to known structures ranked by confidence. ARDL--VIPMIYCGHGY AFDLCDLIPV--CGMAY Sequence of known structure

16 ARDLVIPMIYCGHGY HMM PSI-Blast Hidden Markov Model DB of KNOWN STRUCTURES Hidden Markov Model DB of KNOWN STRUCTURES HMM-HMM matching Phyre2 ARDL--VIPMIYCGHGY AFDLCDLIPV--CGMAY Sequence of known structure 3D-Model

17 ARDLVIPMIYCGHGY HMM PSI-Blast Hidden Markov Model DB of KNOWN STRUCTURES Hidden Markov Model DB of KNOWN STRUCTURES HMM-HMM matching Phyre2 ARDL--VIPMIYCGHGY AFDLCDLIPV--CGMAY Sequence of known structure Very powerful – able to reliably detect extremely remote homology Routinely creates accurate models even when sequence identity is <15% 3D-Model


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