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Homology Modelling
Homology Modelling
Assignment 2
Dated: May 5, 2020
DEPARTMENT OF BIOINFORMATICS
COMSATS UNIVERSITY ISLAMABAD
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Swiss model
SWISS-MODEL is a structural bioinformatics web-server dedicated
to homology modeling of 3D protein structures. Homology modeling is currently the
most accurate method to generate reliable three-dimensional protein structure models
and is routinely used in many practical applications.
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STEP 1
First access the SWISS-MODEL website and click "Start modelling" to start a new
modelling project.
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STEP 2
Click on “Start Modelling” and provide your target protein. You can either paste the
protein sequence or provide the UniprotKB AC (P96134) of your target sequence in the
input form. A project title is automatically suggested if a UniProtKB AC is used.
STEP 3
Click on “Search For Templates” button to search for available template
structures. Once the search is started, you can wait and verify the status of the job or
you can bookmark the page using the provided link and visualize the results later. When
the template search is finished, the output page includes a table showing the list of
available templates ranked according to the expected quality of the resulting models.
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The table below contains multiple templates which cover the complete sequence and
share a considerable sequence identity with our target sequence.
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STEP 4
Let's rank them according to their coverage to the target sequence, and let's
select the top-ranking templates.
Step 5
I selected template number 2 (319y. 1 .A) which shows a sequence identity of
67.97% with our target sequence.
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STEP 6
The final step is to build homology model using the selected template by
clicking on “Build Model” button.
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MODEL RESULTS
For each model generated based on the selected templates, the following information is
provided:
A file containing the model coordinates along with relevant information on the
modelling process
The oligomeric state of the model
The modelled ligands
QMEAN model quality estimation results
The target–template sequence alignment
The template name (SMTL ID)
The sequence identity to the target
The target sequence coverage
Models can be displayed interactively using the 3D viewer. By default, models are
colored by model quality estimates assigned by QMEAN to highlight regions of the
model which are well- or poorly modelled.
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PDB FORMAT
TITLE SWISS-MODEL SERVER (https://swissmodel.expasy.org)
TITLE 2 SODC_DROME P61851 Superoxide dismutase [Cu-Zn]
EXPDTA THEORETICAL MODEL (SWISS-MODEL SERVER)
AUTHOR SWISS-MODEL SERVER (SEE REFERENCE IN JRNL Records)
REVDAT 1 06-MAY-20 1MOD 1 02:38
JRNL AUTH
A.WATERHOUSE,M.BERTONI,S.BIENERT,G.STUDER,G.TAURIELLO,
JRNL AUTH 2 R.GUMIENNY,F.T.HEER,T.A.P.DE
BEER,C.REMPFER,L.BORDOLI,
JRNL AUTH 3 R.LEPORE,T.SCHWEDE
JRNL TITL SWISS-MODEL: HOMOLOGY MODELLING OF PROTEIN
STRUCTURES AND
JRNL TITL 2 COMPLEXES
JRNL REF NUCLEIC.ACIDS.RES.. V. 46 W296
2018
JRNL PMID 29788355
JRNL DOI 10.1093/nar/gky427
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH S.BIENERT,A.WATERHOUSE,T.A.P.DE
BEER,G.TAURIELLO,G.STUDER,
REMARK 1 AUTH 2 L.BORDOLI,T.SCHWEDE
REMARK 1 TITL THE SWISS-MODEL REPOSITORY - NEW FEATURES AND
FUNCTIONALITY
REMARK 1 REF NUCLEIC.ACIDS.RES.. V. 22
2017
REMARK 1 REFN ISSN 0305-1048
REMARK 1 PMID 27899672
REMARK 1 DOI 10.1093/nar/gkw1132
REMARK 1
REMARK 1 REFERENCE 2
REMARK 1 AUTH N.GUEX,M.C.PEITSCH,T.SCHWEDE
REMARK 1 TITL AUTOMATED COMPARATIVE PROTEIN STRUCTURE
MODELING WITH
REMARK 1 TITL 2 SWISS-MODEL AND SWISS-PDBVIEWER: A HISTORICAL
PERSPECTIVE
REMARK 1 REF ELECTROPHORESIS V. 30
2009
REMARK 1 REFN ISSN 0173-0835
REMARK 1 PMID 19517507
REMARK 1 DOI 10.1002/elps.200900140
REMARK 1
REMARK 1 REFERENCE 3
REMARK 1 AUTH P.BENKERT,M.BIASINI,T.SCHWEDE
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