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Prediction of Protein Structures, Functions, and Interactions

ISBN: 978-0-470-51767-3
302 pages
December 2008
Prediction of Protein Structures, Functions, and Interactions (0470517670) cover image
The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization.

Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include:

  • first steps of protein sequence analysis and structure prediction
  • automated prediction of protein function from sequence
  • template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling
  • template-free prediction of three-dimensional protein structures
  • quality assessment of protein models
  • prediction of molecular interactions: from small ligands to large protein complexes
  • macromolecular docking
  • integrating prediction of structure, function, and interactions

Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.  

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List of Contributors.

Preface.

1 The Basics of Protein Sequence Analysis (Katarzyna H. Kaminska, Kaja Milanowska and Janusz M. Bujnicki).

2 First Steps of Protein Structure Prediction (Karolina Majorek, Łukasz Kozłowski, Marcin Jąkalski and Janusz M. Bujnicki).

3 Automated Prediction of Protein Function from Sequence (Meghana Chitale, Troy Hawkins and Daisuke Kihara).

4 Template Based Prediction of Three-dimensional Protein Structures: Fold Recognition and Comparative Modeling (Jan Kosiński, Karolina L. Tkaczuk, Joanna M. Kasprzak and Janusz M. Bujnicki).

5 Template-free Predictions of Three-dimensional Protein Structures: From First Principles to Knowledge-based Potentials (Dominik Gront, Dorota Latek, Mateusz Kurcinski and Andrzej Kolinski).

6 Quality Assessment of Protein Models (Björn Wallner and Arne Elofsson).

7 Prediction of Molecular Interactions from 3D-structures: From Small Ligands to Large Protein Complexes (Kengo Kinoshita, Hidetoshi Kono and Kei Yura).

8 Structure-based Prediction of Enzymes and Their Active Sites (James W. Torrance and Janet M. Thornton).

9 The Prediction of Macromolecular Complexes by Docking (Sjoerd J. de Vries, Marc van Dijk and Alexandre M.J.J. Bonvin).

10 Protein Function Prediction via Analysis of Interactomes (Elena Nabieva and Mona Singh).

11 Integrating Prediction of Structure, Function, and Interactions (Michael Tress, Janusz M. Bujnicki, Gonzalo Lopez and Alfonso Valencia).

Index.

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Professor Bujnicki is head of the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology, Warsaw, Poland. He is the editor of “Practical Bioinformatics" (Springer-Verlag, 2004).
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