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 Cn3D is NCBI's 3D structure viewer. Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application.

With version 4, Cn3D is now a complete multiple alignment editor as well, and includes algorithms for aligning sequences to other sequences and to structures. You can now create and even annotate multiple alignments. Cn3D is used as the primary alignment curation tool for the CDD project.





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