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Cn3D: sequence and structure views for Entrez

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Viewing structure and sequence

In addition to working as a 3D-structure viewer, Cn3D now provides interactive viewing of sequences and sequence alignments. Amino acid (or nucleotide) residues, selected in the structure window by a ‘double click’ of the mouse, are automatically highlighted in the sequence window, and vice versa. Using this highlighting tool, it is possible to map functional sites between structure and sequence. Selecting residues located at the intermolecular interface of a protein–DNA complex, for example,

Viewing structure neighbors

Each protein chain and domain in MMDB has been compared with the others in the database using VAST, a 3D-structure comparison and alignment algorithm5. Similarities crossing a significance threshold are recorded in Entrez and can be viewed by selecting ‘structure neighbors’. The structure window of Cn3D will display the 3D superposition with one or more neighbors, while the sequence window shows a sequence view of the structural alignment. Cn3D provides controls to ‘hide’ individual neighbors

Customizing the display

3D structure can provide a wealth of information about macromolecular function and evolution. However, viewing all the atoms of large macromolecules can be confusing, and an important task for a molecular-graphics viewer is often to hide extraneous detail. To address this issue, Cn3D provides controls that focus the display on a region or feature of interest. One control allows the user to ‘hide’ chains, domains or residues that obscure that feature. A more powerful control allows the user to

Availability

Cn3D is freely distributed by NCBI. Versions for Windows, Macintosh and UNIX computers can be downloaded from the internet address listed in Box 1. To work with Entrez, Cn3D must be configured as a ‘helper application’ for the user’s World Wide Web browser. For PC platforms a ‘one-click’ installation procedure automatically sets the necessary browser parameters. For other platforms simple instructions are provided on Cn3D’s ‘help’ pages (Box 1).

Special services

Cn3D is also used by two special- purpose servers supported by NCBI. The VAST-Search service (see Box 1) allows structural biologists to compare newly determined structures with those already present in MMDB. Search results are presented to the user as a list of structure neighbors, just as in Entrez, and can be viewed with Cn3D. For the NCBI genome analysis service (Box 1), all open reading frames in completely sequenced microbial genomes are compared with sequences in MMDB using the BLAST

Acknowledgements

We thank the NCBI structure group for their work in testing Cn3D versions 2.0 and 2.5. We also thank Patrick Durand, Jim Ostell, Tatiana Tatusova, Denis Vakatov, David Wheeler and the NCBI software group for useful criticism and help with the software toolkit. We thank the NIH Intramural Research Program for support.

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