Biol 6312

1 May 2018

Lesson 10:

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

Fully automated 3-d structure prediction is available at several web servers: Examples of results Fig. 4-26, Fig. 4-27

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:

I-TASSER (Reference)

TASSER-Lite server

MULTICOM (Reference)

Phyre2 Imperial Cancer Research Fund, London: Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] new reference 2015

MetaTASSER Jeffrey Skolnick, Georgia Tech (appears to be down, new services page here)

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
C1, 1-399
March 2018

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

Last modified April 29, 2018