Structure prediction
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TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN - PowerPoint PPT Presentation


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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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Structure prediction

TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN

At present, there is still no method available

that can consistently predict correct structure from

a general sequence

NCKU


Homology modeling
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


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



Raw sequence

Use templates to build

the structure of the homologous

sequence

Predicted structure

NCKU


Use swisspdbviewer as an example to build a structure of the following sequence
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


NCKU following sequence


NCKU following sequence


NCKU following sequence


NCKU following sequence


NCKU following sequence


NCKU following sequence


1TNRA following sequence

DOGB

NCKU


NCKU following sequence


Before magic fit following sequence

After magic fit

NCKU


Activate the raw sequence following sequence

NCKU


NCKU following sequence


The preliminary result following sequence

NCKU


Jenn kang hwang dept of biological science technology national chiao tung university

Structural Bioinformatics System following sequence

Jenn-Kang Hwang

Dept of Biological Science & Technology

National Chiao-Tung University

NCKU


Structural bioinformatics system
Structural Bioinformatics System following sequence

  • Integration of structure database & other bio-databases

  • Structure analysis & Prediction

  • Dynamics & minimization

  • Molecular docking

  • Structure-sequence analysis

  • Integration of analysis tools

NCKU


Dynamics & minimization following sequence

Link to structure database

Molecular visualization

Molecular docking

Structure Analysis & Prediction

NCKU


NCKU following sequence


Vmd abc

VMD following sequenceABC

NCKU


Vmd namd
VMD+NAMD following sequence

NCKU


VMD following sequence

NCKU


NCKU following sequence


NCKU following sequence


NCKU following sequence


NAMD following sequence

NCKU


NCKU following sequence


NCKU following sequence


NCKU following sequence


NCKU following sequence


A sample conf file
A sample Conf file following sequence

NCKU


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