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Peer Review

Cn3D Tutorial



Overall Numeric Rating:

4.67 stars
Content Quality: 5 stars
Effectiveness: 4 stars
Ease of Use: 4 stars
Reviewed: Feb 16, 2002 by Biology Editorial Board
Overview: Cn3D is a molecular visualization tool of the NCBI (National Center for Biotechnolgy Information). The Cn3D program is available for download for the Windows, Macintosh, and various UNIX platforms. Cn3D reads modified PDB files in the format of the Molecular Modeling Database (MMDB). Unlike Chime or Protein Explorer, which run as a plug-in on a browser, a program needs to be downloaded onto your computer to use Cn3D. The program permits the simultaneous viewing of the primary and secondary structures of a macromolecule along with its 3D structure, using two separate windows. This nifty feature allows one to easily make correlations of structure and sequence, for example in determining the amino acids that make up a ligand binding pocket. The 3D window contains drop down menus that allow the user to change the rendering of the molecule to emphasize desired views. Homologous sequences can be aligned and their 3D structures superimposed for viewing. Cn3D offers features not available in most other molecular visualization freeware, and is recommended as a valuable addition for use in classes in biochemistry, genetics, bioinformatics, and evolution, as well as being a useful tool for researchers.
Type of Material: Interactive program
Target Student Population: Any level of college student in biochemistry, genetics, bioinformatics, and evolution

Evaluation and Observation

Content Quality

Rating: 5 stars

Quality of Content Ratings: (5) (5) = (5.0)

  • An excellent research grade program made available for free as a downloaded program.

  • A complete suite of modeling applications.

  • Linked to major databases in NCBI which can be searched with ENTREZ.

  • Online instructional tutorial.

  • Demonstration molecule easy to load.

  • The menus available in the 3D viewing window allow the user to render the molecule in a variety of useful ways. The settings for the predefined renderings can be manipulated by the user.

  • Linked to major databases in NCBI. These can be searched with ENTREZ, or molecules may be accessed via PDB (Protein Data Bank) codes.

  • The ability to compare different structures is a powerful visualization tool for studies of sequence and structural homology.

  • None

Potential Effectiveness as a Teaching Tool

Rating: 4 stars

Potential Effectiveness as a Teaching-Learning Tool Ratings: (4) (4.5) = (4.25)

  • A good supplement to a text or used as a stand-alone module.

  • Highly interactive, inquiry-based and open-ended.

  • Would be possible to write questions based upon structures being viewed.

  • Novel, dual viewing windows for primary/secondary structure and 3D structure.

  • Especially good for coupling structural comparisons and sequence alignments

  • A valuable addition to the suite of tools available for bioinformatic analysis

  • Proper background for the use of the program needs to be provided for most undergrads

  • Not linked to educational tutorials. It might be easy for students to get lost in analyzing a structure for the first time without some guidance.

  • While this program is excellent for researchers, a little more background on molecular modeling would help students.

  • Can be a bit overwhelming for students at first, and may require assignment of a specific tutorial or problem to solve to keep students on task.

Ease of Use for Both Students and Faculty

Rating: 4 stars

Ease of Use Ratings: (4) (4) = (4.0)

  • Easy to navigate and quick, without any defective links or bugs.

  • Point and click manipulations of structures, no need to enter commands line by line.

  • Linked to searchable database through ENTREZ.

  • The menus in both the primary/secondary structure and 3D structure windows are easy to use and, for the most part, self explanatory

  • Graphics are superb, and provide for easy correlation of primary, secondary, and tertiary structures

  • If an instructor wishes to use this program in a computer lab, the Cn3D must be downloaded and installed on each computer.

  • Undergraduates will need some hands on tutoring on the use of the program

  • Not linked to educational tutorials, would require some training for students to be able to use this program independently.