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F. DiMaio, A. Soni & J. Shavlik (2008).
Machine Learning in Structural Biology: Interpreting 3D Protein Images. In S. Mitra, S. Datta, T. Perkins & G. Michailidis, editor, Introduction to Machine Learning and Bioinformatics, pp. 237-276. Chapman & Hall/CRC Press.
(The on-line version is a pre-publication version of the chapter)

This publication is available in PDF.


This chapter discusses an important problem that arises in structural biology: given an electron density map - a three-dimensional 'image' of a protein produced from crystallography - identify the chain of protein atoms contained within the image. This introduction describes in detail the problem of density map interpretation, a background on the algorithms used in automatic interpretation, and a high-level overview of automated map interpretation. The chapter also describes four methods in detail, presenting them in chronological order of development and concludes with a discussion of the advantages and shortcomings of each method, as well as future research directions.

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