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Phyre2

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

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

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

  3. How does Phyre2 work?

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

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

  6. Phyre2 ~ 65,000 known 3D structures

  7. Phyre2 ~ 65,000 known 3D structures

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

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

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

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

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

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

  14. 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

  15. 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

  16. 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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