Protein Explorer Literature


  1. How to cite Protein Explorer (PE)
  2. Papers by Eric Martz et al. about PE
  3. What are other people saying about PE?
  4. Bioinformatics Databases that Display Results in PE
  5. Publications that cite PE


  6. About Protein Structure

The primary citation for Protein Explorer is:
Martz, E. 2002. Protein Explorer: Easy Yet Powerful Macromolecular Visualization, Trends in Biochemical Sciences, 27 (February):107-109.

Please be sure to include the above URL.

(PDF available on request.)

(PE was first released in October, 1998, and has been enhanced frequently since then. See Version History.)

  Papers by Eric Martz et al. about PE, molecular visualization and structural bioinformatics.

  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 ConSurf) in September 2002.

  Bioinformatics Databases that Present Results with Protein Explorer

  Publications that Cite Protein Explorer (last updated in 2003)
    most located with, by advanced searching of full text for the phrase "Protein Explorer".

    Research Discovery in PE

  1. 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".

  2. Wong, K et al. (2003) Mutational and Functional Analysis of a Segment of the Sigma Family Bacteriophage T4 Late Promoter Recognition Protein gp55. J. Biol. Chem. 278:7073-80. "The Noncovalent Bond Finder Module of Protein Explorer and visual inspection was used to assess the effects of gp55 mutation."

  3. 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 Protein Explorer were used to visualize the three-dimensional structures as well as to conduct structure comparisons of different family proteins."

  4. 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".

  5. Gruenke JA, Armstrong RT, Newcomb WW, Brown JC, White JM (March 2002) New Insights into the Spring-Loaded Conformational Change of Influenza Virus Hemagglutinin. J. Virol. 76:4456-66. Used PE's MSA3D for Fig 10C. Also used PE to explore disulfide bridges and cation-pi interactions.

  6. 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. Chem. Biol. 9:1209-1217. Protein Explorer was used to analyze pi-pi interactions between tyrosine and adenine ligand in 281 protein complexes.

  7. Scheper EJ and CG Proud (2002). 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.

  8. Gaucher, EA, et al. (2001). 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).

  9. 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)

  10. 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. More ....

  11. Feig AL, Jabri E (July 2002) Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum. 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.)

  12. Champion, PA et al. (Sept 2006). C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis. Science 313:1632-6. Figure 1F was made with Protein Explorer.

    [Literature has not been searched since 2003.]

  13. Schwartz, A et al. (July 2003). The functional anatomy of an intrinsic transcription terminator. EMBO J. 22:3385-94. Figure 6 was made with Protein Explorer.

  14. 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.

  15. 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.

  16. Nongthomba, U et al. (May 2003) Suppression of Muscle Hypercontraction by Mutations in the Myosin Heavy Chain Gene of Drosophila melanogaster. Genetics 164:209-22.

  17. 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.

  18. 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.

  19. 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. Genetics 163:447-52. Figure 1 was made in part with Protein Explorer.

  20. 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.

  21. 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.

  22. Liu X, Dai S, Crawford F, Frugé R, Marrack P, Kappler J (June 2002) Alternate interactions define the binding of peptides to the MHC molecule IAb. PNAS 99:8820-5. Fig. 3 was created with PE.

  23. Moore, GL and CD Maranas (June 2002) 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.

  24. Fremont, DH et al. (April 2002) Structural Basis of Cytochrome c Presentation by IEk. J. Exp. Med. 195:1043-52. PE was used to make one figure.

  25. Blondin, L et al. (December 2001) 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.

  26. Maguire BA, Zimmermann RA (March 2001). The ribosome in focus. Cell 104:813-816. Figure 4 was made by Wayne A. Decatur using Protein Explorer.

  27. Yoshikawa, DM et al. (March 2001) Characterization of a Phospholipase Cb 2-Binding Site Near the Amino-terminal Coiled-coil of G Protein bg Subunits. J. Biol. Chem. 276:11246-51. PE was used to make Fig. 8.

  28. Chauhan, HJ, et al. (2000) 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.

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