Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2003 Apr-May;55(4-5):249-55.
doi: 10.1080/1521654031000123385.

Target selection and determination of function in structural genomics

James D Watson  1 , Annabel E Todd, James Bray, Roman A Laskowski, Aled Edwards, Andrzej Joachimiak, Christine A Orengo, Janet M Thornton
Affiliations
Review

Target selection and determination of function in structural genomics

James D Watson et al. IUBMB Life. 2003 Apr-May.

Abstract

The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Outline of the target selection protocol for MCSG. Algorithms and functional databases are italicised (see text for references). For simplicity, methods for handling domains within sequences are not addressed in the diagram.
Figure 2
Figure 2
Outline of the semi-automated functional analysis pipeline we have developed, illustrating the types of information that can be inferred from the combination of procedures.
Figure 3
Figure 3
The various ‘success’ levels of each of the major stages in our functional analysis pipeline are shown. The results are based on the analysis of 24 out of 60 deposited MCSG structures.
See this image and copyright information in PMC

References

    1. Terwilliger TC. Structural genomics in North America. Nat. Struct. Biol. Structural Genomics Supplement. 2000 Nov;2000:935–939. - PubMed
    1. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S. Structural genomics projects in Japan. Nat. Struct. Biol. Structural Genomics Supplement. 2000 Nov;2000:943–945. - PubMed
    1. Zhang C, Kim S-H. Overview of structural genomics: from structure to function. Curr. Opin. Chem. Biol. 2003;7:28–32. - PubMed
    1. Burley K. An overview of structural genomics. Nat. Struct. Biol. Structural Genomics Supplement. 2000 Nov;2000:932–934. - PubMed
    1. Blundell T, Mizuguchi K. Structural genomics: an overview. Prog. Biophys. Mol. Biol. 2000;73:289–295. - PubMed