The primary citation for Protein Explorer is:
Martz, E. 2002. Protein Explorer: Easy Yet Powerful
Macromolecular Visualization, Trends in Biochemical Sciences,
Please be sure to include the above URL.
(PDF available on
(PE was first released in October, 1998,
and has been enhanced frequently since then. See
Papers by Eric Martz et al. about PE, molecular visualization and
- Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz,
Eran Bacharach and Tal Pupko, 2007.
Selecton 2007: advanced models for detecting positive and purifying
selection using a Bayesian inference approach,
Nucleic Acids Research 35:W506-W511.
[Free Full Text]
- Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian
Glaser, Eric Martz, Tal Pupko, and Nir Ben-Tal,
2005. ConSurf 2005: the projection of evolutionary
conservation scores of residues on protein structures,
Nucleic Acids Research 33:W299-W302.
- Martz, Eric, and Timothy Driscoll, 2004. "Introduction to
Macromolecular Visualization", in The Internet for Molecular
Biologists: A Practical Approach, Clare E. Sansom and Robert M.
Horton, eds., Oxford University Press, Chapter 9, pp. 161-189.
- Martz, Eric, 2004, "Visualization, Molecular" plus
other entries for the Dictionary of Bioinformatics
and Computational Biology,
John M. Hancock and Marketa J. Zvelebil, eds., Wiley-Liss Publishers.
- Duncan, Gary A., Eric Martz, and Sam Donovan, 2003. "Proteins:
historians of life on earth", in "Microbes count! Problem posing, problem
solving, and peer persuasion in microbiology", John R. Jungck, Marion Field
Fass, and Ethel D. Stanley, eds. BioQUEST Curriculum Consortium, pp. 181-190.
(Available through the American Society of Microbiology Press,
- Martz, Eric, 2003. "3D Molecular Visualization with Protein
Chapter 32, pages 565-586
in Introduction to Bioinformatics, Stephen A. Krawetz
and David D. Womble, eds,
Humana Press, Totowa NJ.
(Includes Challenges to help you learn Protein Explorer
based on myoglobin and lipase.)
- Glaser, Fabian, Tal Pupko, Inbal Paz, Rachel E. Bell,
Eric Martz, and Nir Ben-Tal. January 2003.
ConSurf: Identification of Functional Regions in Proteins by
Surface-Mapping of Phylogenetic Information.
- Martz, Eric. 2002. Protein Explorer: Easy Yet Powerful
Macromolecular Visualization, Trends in Biochemical Sciences,
(PDF available on
- Martz, Eric. 2000. Protein Explorer: Freeware for 3D
visualization of macromolecular structure, FASEB J. 14:22
What Are People Saying About Protein Explorer?
Protein Explorer was a Hot Pick in Science's Netwatch in
September 2000, and again (for results of
- "Protein Explorer has revolutionized the teaching of biology
at a molecular level",
MERLOT Classics Award for Biology, September 2003.
- "Protein Explorer worked very well in these assignments",
and was "user-friendly"
say David Honey and James Cox, who chose Protein Explorer for the protein
exploration segment of their large biochemistry class at
Murry State University, Murray KY US (fall 2003). See their detailed
- "I am having a great time with my students and Protein Explorer.
... I have used RasMol in the past and this is much more visual and user
friendly ---especially for my [AP] HS students. I am glad I took the time to
Mary Ann Rall, Torrey Pines High School, San Diego CA,
USA, September 2003.
"This is a dream for communicating with chemists. This is unbelievable!"
Rajiv Chopra, crystallographer, Wyeth Pharmaceuticals, July 2003, upon seeing
Protein Explorer's contact surfaces display for the first time.
"PE is not only interesting for students but also for research. It is a very
easy to learn tool. It took to me only 1 hour to teach my students how to find
non-covalent interactions and evolutionary patterns. They find it very easy to
use in comparison with RasMol and SwissPdb-Viewer."
Dept. Bioquimica i Biotecnologia,
Univ. Rovira i Virgili
Spain (European Union). June 2003.
- "I've used Rasmol, O and Weblab Viewer Pro in the past and Protein
Explorer is much easier to use. I want to incorporate more visualization
into the biochemistry course ... I decided to use Protein Explorer because
it's the easiest molecular visualization program I've seen."
(Mark Reynolds, professor at St. Joseph's University, Philadelphia
Pennsylvania USA, February 2003.)
- "PyMol is very pretty, but way too complicated".
(Steven Sandler, who uses Protein Explorer in his research, on his Intel Mac,
and who is a professor in the Dept. Microbiology at the University of
Massachusetts, Amherst, January 2007.)
- "Protein Explorer is the most user-friendly program I have
ever encountered. Usually when you leave the class, you're afraid
to try it, but I'm not afraid to go back and try this".
(Hortense Brice, Teacher at Whitney Young High School, Chicago IL US,
after a two-day Protein Explorer workshop within a
SEPA Course in Milwaukee,
- "Research grade .... especially useful in student-run investigations of
macromolecular structure. .... Highly interactive, inquiry-based
and open-ended. Would be possible to write questions based upon
structures being viewed, as seen in
Lesson Plans link."
The MERLOT Biology Review
Panel rated Protein Explorer Five Stars
in all 3 categories (Quality, Teaching Tool, Ease of Use)
in January, 2002.
- An "impressive integrated knowledge base"
is how Protein Explorer
is described by Gkoutos, Murray-Rust, Rzepa, Viravaidya and Wright
"The Application of XML Languages for Integrating Molecular Resources",
Internet Journal of Chemistry, November 2001.
- "... spectacular views of intermolecular interactions ....
Overall, PE is a powerful addition to the suite of RasMol-based
Marcey, David J.,
"Molecular Visualization for the Masses",
BioMedNet issue 90, 2000.
- "One look at the demonstration of calmodulin complexing with calcium is
a convincing lesson on the impact of multimedia in teaching protein structure
and function. The concept of induced fit is given a new life by viewing
proteins in full animation."
Parslow, G. R., in "Websites of note",
Biochem. Mol. Biol. Education 29:156, 2001.
Bioinformatics Databases that Present Results with Protein Explorer
- The Protein Data Bank operated by the
Research Collaboratory for Structural Bioinformatics (USA) offered
Protein Explorer from 1999-2005.
- Probable Quaternary Structure at
the European Bioinformatics Institute, Hinxton UK.
Database of Macromolecular Movements, Yale University, New Haven,
- OCA, a
search interface and browser for macromolecular structure and function,
Weizmann Institute of Science, Rehovot, Israel.
- Finding 3-D Similarities in Protein Structures by
Combinatorial Extension, San Diego Supercomputer Center,
- ConSurf, a server
for the identification of functional regions in proteins as conserved
or hypermutable patches. Tel-Aviv University, Israel.
- Biology Workbench,
integrated access to sequence and structure databases with result
San Diego Supercomputer Center, California, USA.
Biology Student Workbench, a simplified version of the
Biology Workbench designed for students. (Protein Explorer
is described on its
Resources and Links page.)
HIV Macromolecular Structures, a component of the Sequence Database
HIV Databases at Los Alamos
National Laboratory, Los Alamos, New Mexico USA.
Publications that Cite Protein Explorer
(last updated in 2003)
most located with highwire.stanford.edu,
by advanced searching of full text for the phrase "Protein Explorer".
Research Discovery in PE
Miller, S et al. (2003)
The closed structure of the MscS mechanosensitive
channel-cross-linking of single cysteine mutants.
J. Biol. Chem. In press.
Regarding Fig. 1: "The images were created and inter-residue
distances measured using MDL Chime via Protein Explorer".
Wong, K et al. (2003)
Mutational and Functional Analysis of a Segment of the
Sigma Family Bacteriophage T4 Late Promoter Recognition
J. Biol. Chem. 278:7073-80.
Noncovalent Bond Finder Module of Protein Explorer and visual inspection
was used to assess the effects of gp55 mutation."
Hsu SY, Nakabayashi K, and A Bhalla (2002)
Evolution of Glycoprotein Hormone Subunit Genes in Bilateral Metazoa:
Identification of Two Novel Human Glycoprotein Hormone Subunit Family
Genes, GPA2 and GPB5.
Mol. Endocrinol. 16:1538-51.
"The SWISS PDB VIEWER and
were used to visualize the three-dimensional structures
as well as to conduct structure comparisons of different
Bottoms CA, Smith PE, Tanner JJ (2002) A structurally conserved water molecule
in Rossmann dinucleotide-binding domains.
Protein Sci. 11:2125-37.
Concerning this paper, Bottoms said
"We described a 'structurally conserved
water molecule' that I first noticed while using Protein Explorer." He adds
"When I really want to 'see a protein', I use Protein Explorer ... the best
I've found for studying individual macromolecules qualitatively".
Gruenke JA, Armstrong RT, Newcomb WW, Brown JC, White JM
New Insights into the Spring-Loaded Conformational Change of Influenza
J. Virol. 76:4456-66.
Used PE's MSA3D for Fig 10C. Also used PE to explore disulfide bridges
and cation-pi interactions.
Boehr DD, Farley AR, Wright GD, Cox JR (2002).
Analysis of the pi-pi Stacking Interactions between the Aminoglycoside
Antibiotic Kinase APH(3')-IIIa and Its Nucleotide Ligands.
Protein Explorer was used to analyze pi-pi interactions between
tyrosine and adenine ligand in 281 protein complexes.
Scheper EJ and CG Proud
Does phosphorylation of the cap-binding protein eIF4E play a role
in translation initiation?
Eur. J. Biochem. 269:5350-9.
Used PE to measure interatomic distances.
Gaucher, EA, et al.
Function-structure analysis of proteins using covarion-based
evolutionary approaches: Elongation factors.
Proc. Natl. Acad. Sci. US 98:548-52.
PE was used for structure visualization (but no published figures).
Granovsky, AE, and NO Artemyev (2000).
Identification of the gamma Subunit-interacting Residues on
Photoreceptor cGMP Phosphodiesterase, PDE6-alpha'
J. Biol. Chem. 275:41258-62.
One panel in Figure 5 was made with Protein Explorer's MSA3D to color
by multiple sequence alignment, showing levels of conservation.
Teaching with PE
(See Lesson Plans)
- Honey DW, Cox JR (Sept/Oct 2003)
Lesson Plan for Protein Exploration in a Large Biochemistry Class.
Biochem. Mol Biol. Ed. 31:356-366.
In classes with 50-60 students, a series of investigations are assigned
that emphasize finding noncovalent interactions using Protein Explorer.
Three assignments with questions are detailed in this paper.
- Feig AL, Jabri E (July 2002)
Incorporation of Bioinformatics Exercises into the Undergraduate
Biochem. Mol Biol. Ed. 30:224-231.
PE is used extensively in their courses. Contact
See also Lesson Plans for Protein Explorer.
Figures Made with PE
(PE is designed for real-time interaction, not for publication-quality images.
Nevertheless, in some cases illustrated by the publications cited below,
satisfactory results can be
obtained. See Printing publication-quality images in PE.)
Champion, PA et al. (Sept 2006).
C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis.
Figure 1F was made with Protein Explorer.
[Literature has not been searched since 2003.]
Schwartz, A et al. (July 2003).
The functional anatomy of an intrinsic transcription
EMBO J. 22:3385-94.
Figure 6 was made with Protein Explorer.
Meyer, PR et al. (June 2003).
Relationship between 3'-Azido-3'-Deoxythymidine Resistance and
Primer Unblocking Activity in Foscarnet-Resistant Mutants of Human
Immunodeficiency Virus Type 1 Reverse Transcriptase.
J. Virol. 77:6127-37.
Figure 1 is the
most impressive one created with Protein Explorer that I've
seen in a research publication.
Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP (May 2003)
RNA-modifying machines in archaea.
Mol. Microbiol. 48:617-629.
Coauthor Decatur confirms that Protein Explorer was used to make
Fig. 5 though it is not cited.
Nongthomba, U et al. (May 2003)
Suppression of Muscle Hypercontraction by Mutations in the Myosin
Heavy Chain Gene of Drosophila melanogaster.
Seligman SJ, Bucher DJ (March 2003).
The importance of being outer: consequences of the distinction between the
outer and inner surfaces of flavivirus glycoprotein E.
Trends Microbiol. 11:108-10.
Figures 1 and 2 (surfaces) were made with Protein Explorer.
McIlroy, D et al. (March 2003)
A triple-mutated allele of granzyme B incapable of inducing apoptosis.
Proc. Natl. Acad. Sci. USA 100:2562-7.
Four panels in Figure 5 were created with Protein Explorer,
including two contact surface displays.
Thompson JS et al. (January 2003)
Identification of a Functional Domain Within the Essential Core of Histone H3 That Is Required for Telomeric and HM Silencing in Saccharomyces cerevisiae.
Figure 1 was made in part with Protein Explorer.
Decatur WA, Fournier MJ (July 2002) rRNA modifications and ribosome function.
Trends Biochem. Sci. 27:344-351.
Figs. 2, 3, 4 contain molecular images created with Protein Explorer,
which was also used for
supplementary on-line resources.
Leppla SH, Robbins JB, Schneerson R, Shiloach J (July 2002)
Development of an improved vaccine for anthrax.
J. Clin. Invest. 110:141-144.
Figure 2 was created with PE.
Liu X, Dai S, Crawford F, Frugé R, Marrack P, Kappler J
Alternate interactions define the binding of peptides to the MHC molecule
Fig. 3 was created with PE.
Moore, GL and CD Maranas
eCodonOpt: a systematic computational framework for
optimizing codon usage in directed evolution experiments.
Nucleic Acids Res. 30:2407-16.
PE was used in making Figs. 11 and 13.
Fremont, DH et al.
Structural Basis of Cytochrome c Presentation by IEk.
J. Exp. Med. 195:1043-52.
PE was used to make one figure.
Blondin, L et al.
The second ADF/cofilin actin-binding site exists in F-actin,
the cofilin-G-actin complex, but not in G-actin.
Eur. J. Biochem. 268:6426-34.
PE was used to make Fig. 5.
Maguire BA, Zimmermann RA (March 2001).
The ribosome in focus.
Figure 4 was made by Wayne A. Decatur using Protein Explorer.
Yoshikawa, DM et al.
Characterization of a Phospholipase Cb
2-Binding Site Near
the Amino-terminal Coiled-coil of G Protein
J. Biol. Chem. 276:11246-51.
PE was used to make Fig. 8.
Chauhan, HJ, et al.
Sites of limited proteolysis in the pyruvate decarboxylase
component of the pyruvate dehydrogenase multienzyme complex of
Bacillus stearothermophilus and their role in catalysis.
Eur. J. Biochem. 267:7158-69.
PE was used to make the molecular surfaces in Fig. 9.
Feedback to Eric Martz.