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The Protein Universes

Some Informatic Issues in Protein Classification

  • Chapter
Power Laws, Scale-Free Networks and Genome Biology

Part of the book series: Molecular Biology Intelligence Unit ((MBIU))

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Abstract

We discuss some informatic problems in protein classification. We first address a neglected problem in sequence classification-information loss resulting from alphabet contraction. Since the use of reduced alphabets is a standard bioinformatic tool, this is a significant issue. We review recent work in which it was shown that information theoretic methods can be used to quantitate the amount of structural information carried by a specified sequence representation. These tools are then used to construct reduced alphabets of specified size which retain the maximum possible amount of structural information. We then turn to structure classification. After briefly reviewing previous work in this field, we discuss the fact that sequence and structure classification give different pictures of the protein space. We outline ongoing research in which new parameters are sought which explicitly encode architecture choice by protein sequences.

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Authors and Affiliations

  1. Department of Pharmacology and Biological Chemistry, and Center for Biomathematics, Mount Sinai School of Medicine of New York University, One Gustave L. Levy Place, New York, New York, 10029, USA

    S. Rackovsky

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Rackovsky, S. (2006). The Protein Universes. In: Power Laws, Scale-Free Networks and Genome Biology. Molecular Biology Intelligence Unit. Springer, Boston, MA. https://doi.org/10.1007/0-387-33916-7_11

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