Protein Explorer: easy yet powerful macromolecular visualization

Trends Biochem Sci. 2002 Feb;27(2):107-9. doi: 10.1016/s0968-0004(01)02008-4.


Protein Explorer (PE, enables students, educators and other nonspecialists to visualize macromolecular structures easily. It also offers several advanced capabilities useful to protein structure specialists. Great attention has been given to making PE easy to use. Explanations, color keys and troubleshooting information are displayed automatically. There are also 'Frequently Asked Questions', a one-hour 'Quick-Tour', an alphabetical 'Help/Index/Glossary', and a detailed 'Tutorial'; all making PE much easier to use than either Chime or RasMol. Moreover, it is much more powerful; in addition to basic macromolecular visualization capabilities common to most similar programs, it offers one-click visualization of interfaces between moieties ('contacts'), cation-pi interactions and salt bridges, as well as easy-to-use routines to visualize regions of conservation in three-dimensional protein structures based on multiple sequence alignments.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Computational Biology
  • DNA / genetics
  • Evolution, Molecular
  • Macromolecular Substances
  • Protein Structure, Secondary
  • Proteins / chemistry
  • Proteins / genetics*
  • Sequence Alignment / methods*
  • Sequence Alignment / statistics & numerical data
  • Software


  • Macromolecular Substances
  • Proteins
  • DNA