The molecular structure of living organisms and the complex interactions among its components are the basis for the diversity observed at the macroscopic level. Proteins and nucleic acids are some of the major molecular components, and play a key role in many biological functions, such as those of development and evolution.
In this framework, molecular modeling has been performed using the Cn3D software, created by the US National Center for Biotechnology Information (NCBI). Cn3D is a user-friendly application, which is easy for students to get to know about it with great speed.
Its major advantage is the ability to associate structural with sequence‐related information. For example, the observation of an amino acid alteration due to a mutation can enable a prompt identification of the structural change that this mutation may produce at the protein level. Furthermore, the software allows annotations to structural parts of interest, its graphics are of very high quality and it offers the possibility to draw out many file types, this enables users to produce outputs which may be directly or indirectly used by other applications.
Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. 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 shows structure-structure alignments along with their structure-based sequence alignments, to analyze what regions of a group of related proteins are most conserved in structure and sequence. Custom labeling features, high-quality OpenGL graphics, and a variety of file exports are also included 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.
Cn3D is a Windows, Macintosh and Unix-based software from the United States National Library of Medicine that acts as a helper application for web browsers to view three-dimensional structures from The National Center for Biotechnology Information’s Entrez retrieval service. It “simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features”, according to its official site. Cn3D is in the public domain and its source code is available.
Cn3D shows a representative protein structure, the family alignment, and annotation panels with information about annotated features of the protein family. It highlights the conserved residues in a pattern characteristic to the domain of structure and sequence windows.
Screenshots of the Cn3D and sequence windows are provided at many steps to exemplify the concepts described, they will appear as thumbnail images linked to full-size screen shots. The full-size images are stored in PNG format, depending on the browser used. The Windows version of Cn3D was used to create these images, but aside from platform look-and-feel differences in user interface and window borders, the images will look largely the same on any platform.