PROTEIN STRUCTURE PREDICTION

SOFTWARE/DATABASES
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LECTURE: 13
Instructor: Dr. Muhammad Asif Rasheed
HOMOLOGY MODELING
 MODELLER
 Program mainly in Fortran and Python
 EasyModeller
 Windows executable
 GUI to MODELLER

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HOMOLOGY MODELING
 Swiss-Model
 www.expasy.ch/swissmod
 Allows a user to submit a sequence and get structure
automatically
 Alignment of the query with sequences in PDB using
BLAST
 The user can specify or upload structures as
templates

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HOMOLOGY MODELING
 ModBase
 http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
 3Dcrunch
 www.expasy.ch/swissmod/SWISS-MODEL.html
 WHAT IF
 A program and web interface
 …

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PREDICTION RESULTS
 Should be selected on priority
 Homology with already determined proteins
 Based on good template
 Sequence similarity
 Discard in case of bad template

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THREADING/FOLD RECOGNITION
 I-TASSER
 Combination of ab initio folding and threading
methods
 Structural and function predictions

 Fold recognition

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THREADING/FOLD RECOGNITION
 Lomet server
 Another Zhang lab server

 Based on threading

 Very good results

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THREADING/FOLD RECOGNITION
 SUPERFAMILY
 Hidden Markov modeling
 3D-PSSM
 www.bmm.icnet.uk/ 3dpssm/
 A web-based program
 Structural profile method to identify protein folds
 GenThreader
 http://bioinf.cs.ucl.ac.uk/psipred/index.html
 A web-based program
 A hybrid of the profile and pairwise energy methods

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AB INITIO STRUCTURE PREDICTION
 QUARK
 https://zhanglab.ccmb.med.umich.edu/QUARK/
 Computer algorithm for Ab initio prediction
 Aims to construct the correct protein 3D model

 Amino acid sequence only provided

 Atomic-level knowledge-based force field

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AB INITIO STRUCTURE PREDICTION
 ROBETTA
 http://robetta.bakerlab.org/
 Protein structure prediction service
 Interactive submission interface

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AB INITIO STRUCTURE PREDICTION
 Evfold
 Webserver
 NovaFold
 trRosetta
 Deep learning restraints-guided energy minimization

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AUTHENTICITY OF PREDICTION
 CASP
 Critical Assessment of protein Structure Prediction

 Protein structure prediction every two years

 To test their structure prediction methods

 Independent assessment

 To identifying 3D structure from amino acid

 World championship

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