Chapter

Electron density fitting and structure validation

Mike Carson

in Macromolecular Crystallography

Published in print August 2007 | ISBN: 9780198520979
Published online September 2007 | e-ISBN: 9780191706295 | DOI: https://dx.doi.org/10.1093/acprof:oso/9780198520979.003.0013
 Electron density fitting and structure validation

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The Human Genome Project went three-dimensional in late 2000. ‘Structural genomics’ efforts will determine the structures of thousands of new proteins over the few years. These initiatives seek to streamline and automate every experimental and computational aspect of the structural determination pipeline, with most of the steps involved covered in previous chapters of this volume. At the end of the pipeline, an atomic model is built and iteratively refined to best fit the observed data. The final atomic model, after careful analysis, is deposited in the Protein Data Bank (PDB). About 25,000 unique protein sequences are currently in the PDB. High-throughput and conventional methods will dramatically increase this number and it is crucial that these new structures be of the highest quality. This chapter addresses software systems to interactively fit molecular models to electron density maps and to analyse the resulting models. It is heavily biased toward proteins, but the programs can also build nucleic acid models. The chapter begins with a brief review of molecular modelling and graphics. It then discusses the best current and freely available programs with respect to their performance on common tasks. Finally, some views on the future of such software are given.

Keywords: Human Genome Project; protein sequences; molecular models; electron density maps; software systems

Chapter.  5947 words.  Illustrated.

Subjects: Biochemistry

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