title: Protein Folding
author: Thomas E. Creighton
description: The phenomenon of protein folding has become the focus of intense scientific inquiry. Researchers have realised the importance of understanding how proteins adopt their folding conformations, and are developing experimental techniques to attack this problem. , Protein Folding is a report on the current state of this crucial area of research-the 4y experiments, techniques, and implications of recent findings on modem biotechnology and biomedicine. Its authors are the world's leading investigators in this field, including: R M. Richards, Department of Molecular Biophysics and Biochemistry, Yale University - Janet M Thornton, Biomolecular Structure and Modelling Unit, University College,. . London, UK - Peter L Privokv, Institute of Protein Research, Academy of Sciences, Moscow - Martin Karplus and E. S h, Department of Chemistry, Harvard University - Franz X Schmid, Department of Biochemistry, Universitat Bayreuth, Germany . Oleg B. Ptilsyn, Institute of Protein Research, Academy of Sciences, Moscow Thomas E. Creighton, European Molecular Biology Laboratory, Heidelberg, Germany David P. Goldenberg, Department of Biology, University of Utah - Jean-Renaud Garel, Laboratoire d'Enzymologie du CNRS, Gifsur-Yvette, France - Robert B. Freedman, Biological Laboratory, University of Kent, Canterbury, UK.
zlib_text: C H A P T E R
  5
  Developing Hierarchical 
  Representations for Protein Structures:
  An Incremental Approach
  Xiru Zhang & David Waltz 
  1 Introduction
  The protein folding problem has been attacked from many directions. One
  set of approaches tries to ﬁnd out correlations between short subsequences of
  proteins and the structures they form, using empirical information from crystal-
  lographic databases. AI research has repeatedly demonstrated the importance of
  representation in making these kinds of inferences. In this chapter, we describe
  an attempt to ﬁnd a good representation for protein substructure. Our goal is to
  represent protein structures in such a way that they can, on the hand, reﬂect the
  enormous complexity and variety of different protein structures, and yet on the
  other hand facilitate the identiﬁcation of similar substructures across different
  proteins. Our method for identifying a good representation for protein structure
  is embodied in a program called GENEREP1, which automatic