1 May 2018
Prediction of Tertiary Structure
In general there are three approaches
a) Try to model an amino acid sequence by homology (homology modeling)
b) Try to find compatibility to known structures (threading)
c) Try to fold an amino acid sequence based on physical principles (ab initio or de novo)
Identification of topological fold is often the goal.
Sometimes these approaches are combined
Robetta here (Robot Rosetta)
Kim DE, Chivian D, Baker D.
Protein structure prediction and analysis using the Robetta server.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W526-31.
These sites offer www access to predictions of tertiary structure:
CASP: Critical Assessment of Techniques for Protein Structure Prediction - A regularly held contest to see which prediction methods work the best. It started in 1994. The latest round was CASP12 held in 2016. CASP13 will be held in 2018, with results to be discussed at a conference in December.Twelfth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Proteins: Structure, Function, Bioinformatics Volume 86, Issue S1
Catalog of Structure Prediction Servers
Modeller-download the software for homology modelling
Protein Modeling Site for submitting a protein sequence to several sites at once
See the assignment: HW7
Comments/questions: email me
Copyright 2018, Steven B. Vik, Southern Methodist University