Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers.

• Protein Explorer enables you to see the relations of 3D molecular structure to function. The image can be simplified by hiding everything except the region of interest. A variety of one-click renderings and color schemes help to visualize the backbone, secondary structure, distributions of hydrophobic vs. hydrophilic residues, noncovalent bonding interactions, salt bridges, amino acid or nucleotide sequences, sequence-to-structure mappings and locations of residues of interest, and patterns of evolution and conservation. See the gallery of snapshots of Protein Explorer in action.

• Exploration is done largely from menus and buttons in Protein Explorer's QuickViews interface. The easy user interface means that you do not need to learn any "RasMol command language", although those who have learned some can use it freely.

• Flash movies demonstrate how to use Protein Explorer and what it does. A One-Hour Tour gives beginners an overview of how to use Protein Explorer. Key resources are introduced on Protein Explorer's FrontDoor.

• Explanations, color keys, and help are displayed automatically with each operation you perform. Protein Explorer is a knowledge base with introductory information on many topics about protein structure, such as the origins and limitations of 3D protein structure data, specific oligomers vs. crystal contacts, hydrogen bonds, cation-pi interactions, etc. Protein Explorer includes an extensive help, glossary, index, and reference manual to help you find what you are looking for.

• Educators: Suggestions for lesson plans are included.

• For more about what distinguishes Protein Explorer 2 from RasMol or Protein Explorer 1, see What's New in PE 2?

• Computer requirements: Protein Explorer works on-line in a web browser, and can also be downloaded for off-line use. Just click the QuickStart link on Protein Explorer's FrontDoor and your browser will automatically be checked for compatibility -- if you need to install anything, you will be given instructions. Here are supported computers and browsers. Protein Explorer requires a free browser-plugin, MDL Chime, that renders the 3D molecular image.