Janusz Bujnicki 
Prediction of Protein Structures, Functions, and Interactions 

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.

Table of Content

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, Lukasz Kozlowski, Marcin
J& #261;kalski 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
Kosi& #324;ski, 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.

About the author

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).