Investigating Protein Structure and Evolution with SCOP2

Antonina Andreeva1, Dave Howorth1, Cyrus Chothia1, Eugene Kulesha2, Alexey G. Murzin1

1 MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, 2 European Bioinformatics Institute, Hinxton, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.26
DOI:  10.1002/0471250953.bi0126s49
Online Posting Date:  March, 2015
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Abstract

SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework for the classification of proteins. The SCOP2 classification is described in terms of a directed acyclic graph in which each node defines a relationship of particular type that is represented by a region of protein structure and sequence. The SCOP2 data are accessible via SCOP2‐Browser and SCOP2‐Graph. This protocol unit describes different ways to explore and investigate the SCOP2 evolutionary and structural groupings. © 2015 by John Wiley & Sons, Inc.

Keywords: protein structure; protein evolution; sequence‐structure relationship

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Understanding SCOP2 Evolutionary Relationships Using SCOP2‐Browser
  • Alternate Protocol 1: Understanding SCOP2 Evolutionary Relationships Using SCOP2‐Graph
  • Support Protocol 1: Exploring Evolutionary Events in SCOP2
  • Basic Protocol 2: Understanding SCOP2 Structural Relationships Using SCOP2‐Browser
  • Alternate Protocol 2: Understanding SCOP2 Structural Relationships using SCOP2‐Graph
  • Commentary
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Andreeva, A. and Murzin, A.G. 2006. Evolution of protein fold in the presence of functional constraints. Curr. Opin. Struct. Biol. 16:399‐408.
  Andreeva, A., Howorth, D., Chothia, C., Kulesha, E., and Murzin, A.G. 2014. SCOP2 prototype: A new approach to protein structure mining. Nucleic. Acids Res. 42:D310‐D314.
  Andreeva, A., Howorth, D., Chandonia, J.M., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2008. Data growth and its impact on the SCOP database: New developments. Nucleic. Acids Res. 36:D419‐D425.
  Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic. Acids Res. 28:235‐242.
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  Levitt, M. and Chothia, C. 1976. Structural patterns in globular proteins. Nature 261:552‐558.
  Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536‐540.
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Internet Resources
  http://scop.mrc‐lmb.cam.ac.uk/scop/
  SCOP Structural Classification of Proteins home page.
  http://scop2.mrc‐lmb.cam.ac.uk/
  SCOP2 Structural Classification of Proteins 2 home page.
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