Introduction to Proteomics tools in Homology Modelingweb

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Introduction to Proteomics toolsin Homology
Modeling(web)

• GBA_CSIE_NDHU

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Abstract

• Homology modeling, also known as comparative
  modeling,
• It is a class of methods in protein structure
  prediction.
• The quality of the homology model is dependent on
  the quality of the sequence alignment and
  template structure.
• Current practice in homology modeling is assessed
  in a biannual large-scale experiment known as
  CASP.

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Tools in Expasy

• Protein identification and characterization
• DNA -gt Protein
• Similarity searches
• Pattern and profile searches
• Post-translational modification prediction
• Topology prediction
• Primary structure analysis
• Secondary structure prediction
• Tertiary structure
• Sequence alignment
• Phylogenetic analysis

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Tertiary Structure Prediction

• Homology modeling
• Threading
• Ab initio

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Main Steps of Homology modeling

• identification of structural template
• alignment of target sequence and template
  structure
• model building
• model quality evaluation

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Before Structural Prediction

• Q1sequence alignment?
• Q2structure similar?
• Top Match
• http//topmatch.services.came.sbg.ac.at/

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BLAST Arguments

• Program
• ftp//ftp.ncbi.nlm.nih.gov/blast/executables/LATES
  T/
• Argument
• www.plexdb.org/modules/documentation/NCBIblastall.
  htm

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BLAST Arguments Cont.

• -m alignment view options
• 0 pairwise,
• 1 query-anchored showing identities
• 2 query-anchored no identities
• 3 flat query-anchored, show identities
• 4 flat query-anchored, no identities
• 5 query-anchored no identities and blunt ends
• 6 flat query-anchored, no identities
• 7 XML Blast output
• 8 tabular
• 9 tabular with comment lines, default 0

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Structural Viewer

• Cn3D
• http//www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.sh
  tml
• Rasmol
• www.umass.edu/microbio/rasmol/
• Accelrys DS ViewerPro
• http//accelrys.com/products/discovery-studio/
• Swiss-PdbViewer
• http//spdbv.vital-it.ch/

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Group-assignment

• Q3Please print couple proteins of your
  group-assignment, and use protein structural
  comparison tool to illustrate your statement.
• Q4Using BLASTP to show their local alignment
  with query-anchored and identities.

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Tertiary Structure Prediction

• Homology modeling
• Template selection
• Multiple sequence alignment
• Backbone construction
• Energy minimization
• Evaluation

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Homology Modeling

• SWISS-MODEL
• http//www.expasy.org/swissmod/
• MODELLER
• http//guitar.rockefeller.edu/modeller/
• WHATIF
• http//www.cmbi.kun.nl/whatif/
• InsightII
• http//accelrys.com/products/insight/
• Strap
• http//www.charite.de/bioinf/strap/starting

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Protein Structure Database

• Swiss-Prot
• http//www.uniprot.org/
• Protein Data Bank
• http//www.rcsb.org/pdb/
• SCOP
• http//scop.mrc-lmb.cam.ac.uk/scop/
• CATH
• http//www.cathdb.info/
• DALI
• http//ekhidna.biocenter.helsinki.fi/dali_server/

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Template Search

• BLAST
• http//www.ncbi.nlm.nih.gov/BLAST/
• Fasta3
• http//www.ebi.ac.uk/fasta3/

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Secondary Structure Prediction

• PHD
• http//www.predictprotein.org/
• SOPMA
• http//npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?p
  age/NPSA/npsa_sopma.html
• nnPredict
• http//www.cmpharm.ucsf.edu/nomi/nnpredict.html

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Multiple Sequence Alignment

• ClustalW
• http//www.ebi.ac.uk/clustalw/
• BCM server
• http//searchlauncher.bcm.tmc.edu/

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Model verification

• PROCHECK
• http//www.biochem.ucl.ac.uk/roman/procheck/proch
  eck.html
• BIOTECK
• http//biotech.embl-heidelberg.de8400/
• ProsaII
• http//www.came.sbg.ac.at/Services/prosa.html
• AQUA
• http//www.nmr.chem.uu.nl/users/jurgen/Aqua/server
  /

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ExampleStep-1

• Select a target protein with unknown structure.
• Make sure it is an unknown structure protein.
• BLAST your target protein in database
• gi160799gbAAA29797.1 hemoglobin
• Hit in database with 1ASH

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ExampleStep-2

• 150/333
• Check 1ASH in database
• rest of the residue?

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ExampleStep-3

• Go to Swiss-Model Workspace
• http//swissmodel.expasy.org/SWISS-MODEL.html
• Query your unknown structure protein
• http//swissmodel.expasy.org/workspace/
• Download your predicted model

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ExampleStep-4

• Superimposed your target protein and other
  similar function protein and display them with
  Pdb-Viewer
• http//spdbv.vital-it.ch/
• Dali pairwise comparison
• http//ekhidna.biocenter.helsinki.fi/dali_lite/sta
  rt

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Group-assignment

• Repeat example for your selected protein in last
  group-assignment.
• For example cellulose
• Your assignment should include the following
  terms
• Topic and material
• Selection issue
• Parameters explanation
• 2D alignment comparison
• 3D structure comparison

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Screen capture

• PicPick
• http//picpick.wiziple.net/forum/
• http//playpcesor.blogspot.com/2007/03/picpick-17.
  html