7/14/2015ncku1 ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan structure prediction at present, there...

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03/21/22 NCKU 1 TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN Structure prediction At present, there is still no method available that can consistently predict correct structure fro a general sequence

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Page 1: 7/14/2015NCKU1 TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN Structure prediction At present, there is still no method available that can consistently

04/19/23 NCKU 1

TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN

Structure prediction

At present, there is still no method availablethat can consistently predict correct structure froma general sequence

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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.

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Search for homologues in PDB by BLAST

MQQPMNYPCP QIFWVDSSAT SSWAPPGSVF PCPSCGPRGP DQRRPPPPPP PVSPLPPPSQPLPLPPLTPL KKKDHNTNLW LPVVFFMVLV ALVGMGLGMY QLFHLQKELA ELREFTNQSLKVSSFEKQIA NPSTPSEKKE PRSVAHLTGN PHSRSIPLEW EDTYGTALIS GVKYKKGGLVINETGLYFVY SKVYFRGQSC NNQPLNHKVY MRNSKYPEDL VLMEEKRLNY CTTGQIWAHSSYLGAVFNLT SADHLYVNIS QLSLINFEES KTFFGLYKL

For a raw sequence without a known structure

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Use templates to buildthe structure of the homologoussequence

Predicted structure

Raw sequence

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Use SwissPDBViewer as an Example to build a structure of the following sequence

MQQPMNYPCP QIFWVDSSAT SSWAPPGSVF PCPSCGPRGP DQRRPPPPPP PVSPLPPPSQPLPLPPLTPL KKKDHNTNLW LPVVFFMVLV ALVGMGLGMY QLFHLQKELA ELREFTNQSLKVSSFEKQIA NPSTPSEKKE PRSVAHLTGN PHSRSIPLEW EDTYGTALIS GVKYKKGGLVINETGLYFVY SKVYFRGQSC NNQPLNHKVY MRNSKYPEDL VLMEEKRLNY CTTGQIWAHSSYLGAVFNLT SADHLYVNIS QLSLINFEES KTFFGLYKL

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1TNRADOGB

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Before magic fitAfter magic fit

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Activate the raw sequence

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The preliminary result

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Jenn-Kang Hwang

Dept of Biological Science & Technology

National Chiao-Tung University

Structural Bioinformatics Structural Bioinformatics SystemSystem

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Structural Bioinformatics Structural Bioinformatics SystemSystem

• Integration of structure database & other bio-databases

• Structure analysis & Prediction

• Dynamics & minimization

• Molecular docking

• Structure-sequence analysis

• Integration of analysis tools

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Link to structure database

Structure Analysis & PredictionMolecular visualization

Molecular docking

Dynamics & minimization

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VMD ABC

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VMD+NAMD

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VMD

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NAMD

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