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TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN

Structure prediction. TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN. At present, there is still no method available that can consistently predict correct structure from a general sequence. Homology Modeling. If the sequence identity between two sequences A and B is greater than 25%,

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TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN

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  1. Structure prediction TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN At present, there is still no method available that can consistently predict correct structure from a general sequence NCKU

  2. Homology Modeling If the sequence identity between two sequences A and B is greater than 25%, and if B has a known structure, then it is possible to predict the structure of the sequence A by homology modeling method. NCKU

  3. For a raw sequence without a known structure MQQPMNYPCP QIFWVDSSAT SSWAPPGSVF PCPSCGPRGP DQRRPPPPPP PVSPLPPPSQ PLPLPPLTPL KKKDHNTNLW LPVVFFMVLV ALVGMGLGMY QLFHLQKELA ELREFTNQSL KVSSFEKQIA NPSTPSEKKE PRSVAHLTGN PHSRSIPLEW EDTYGTALIS GVKYKKGGLV INETGLYFVY SKVYFRGQSC NNQPLNHKVY MRNSKYPEDL VLMEEKRLNY CTTGQIWAHS SYLGAVFNLT SADHLYVNIS QLSLINFEES KTFFGLYKL Search for homologues in PDB by BLAST NCKU

  4. NCKU

  5. Raw sequence Use templates to build the structure of the homologous sequence Predicted structure NCKU

  6. Use SwissPDBViewer as an Example to build a structure of the following sequence MQQPMNYPCP QIFWVDSSAT SSWAPPGSVF PCPSCGPRGP DQRRPPPPPP PVSPLPPPSQ PLPLPPLTPL KKKDHNTNLW LPVVFFMVLV ALVGMGLGMY QLFHLQKELA ELREFTNQSL KVSSFEKQIA NPSTPSEKKE PRSVAHLTGN PHSRSIPLEW EDTYGTALIS GVKYKKGGLV INETGLYFVY SKVYFRGQSC NNQPLNHKVY MRNSKYPEDL VLMEEKRLNY CTTGQIWAHS SYLGAVFNLT SADHLYVNIS QLSLINFEES KTFFGLYKL NCKU

  7. NCKU

  8. NCKU

  9. NCKU

  10. NCKU

  11. NCKU

  12. NCKU

  13. 1TNRA DOGB NCKU

  14. NCKU

  15. Before magic fit After magic fit NCKU

  16. Activate the raw sequence NCKU

  17. NCKU

  18. The preliminary result NCKU

  19. Structural Bioinformatics System Jenn-Kang Hwang Dept of Biological Science & Technology National Chiao-Tung University NCKU

  20. Structural Bioinformatics System • Integration of structure database & other bio-databases • Structure analysis & Prediction • Dynamics & minimization • Molecular docking • Structure-sequence analysis • Integration of analysis tools NCKU

  21. Dynamics & minimization Link to structure database Molecular visualization Molecular docking Structure Analysis & Prediction NCKU

  22. NCKU

  23. VMD ABC NCKU

  24. VMD+NAMD NCKU

  25. VMD NCKU

  26. NCKU

  27. NCKU

  28. NCKU

  29. NAMD NCKU

  30. NCKU

  31. NCKU

  32. NCKU

  33. NCKU

  34. A sample Conf file NCKU

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