A survey of educational uses of molecular visualization freeware

Biochemistry and Molecular Biology Education

Volumn 41, Issue 3, 2013, Pages 193-205

  Craig, Paul A ^a   Michel, Lea Vacca ^a   Bateman, Robert C ^b  

^a ROCHESTER INSTITUTE OF TECHNOLOGY   (United States)

^b William Carey University   (United States)

Author keywords

Assessment of educational activities; Computers in research and teaching; Scholarship of teaching and learning; Using modeling as a research tool for investigating teaching; Using multimedia in the classroom

Indexed keywords

ARTICLE; BIOCHEMISTRY; CHEMICAL STRUCTURE; COMPUTER PROGRAM; COMPUTER SIMULATION; EDUCATION; HUMAN; INFORMATION PROCESSING; METHODOLOGY; PROBLEM BASED LEARNING; STUDENT; TEACHING; UNIVERSITY;

BIOCHEMISTRY; COMPUTER SIMULATION; DATA COLLECTION; FACULTY; HUMANS; MODELS, MOLECULAR; PROBLEM-BASED LEARNING; RESEARCH DESIGN; SOFTWARE; STUDENTS; TEACHING;

EID: 84878188703     PISSN: 14708175     EISSN: 15393429     Source Type: Journal    
DOI: 10.1002/bmb.20693     Document Type: Article

References (42)

1. Richardson, D. C. and Richardson, J. S. (1992) The kinemage: A tool for scientific communication. Protein Sci. 1, 3-9.
2. Richardson, D. C. and Richardson, J. S. (1994) Kinemages-simple macromolecular graphics for interactive teaching and publication. Trends Biochem. Sci. 19, 135-138.
3. Pavkovic, S. F. (2005) Mage: A tool for developing interactive instructional graphics. J. Chem. Educ. 82, 167-171.
4. Sayle, R. A. and Milner-White, E. J. (1995) RasMol: Biomolecular graphics for all. Trends Biochem. Sci. 20, 374-376.
5. Goodsell, D. S. (2005) Representing structural information with RasMol. Curr. Protoc. Bioinformatics 5.4.1-5.4.23.
6. Weiner, S. W., Cerpovicz, P. F., Dixon, D. W., Harden, D. B., Hobbs, D. S., and Gosnell, D. L. (2000) RasMol and mage in the undergraduate biochemistry curriculum. J. Chem. Educ. 77, 401-406.
7. Bernstein, H. J. (2000) Recent changes to RasMol, recombining the variants. Trends Biochem. Sci. 25, 453-455.
8. Chen, V. B., Davis, I. W., and Richardson, D. C. (2009) KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program. Protein Sci. 18, 2403-2409.
9. Horton, R. M. (1999) Scripting wizards for chime and RasMol. Biotechniques 26, 874-876.
10. Cammer, S. A. (2000) SChiSM: Creating interactive web page annotations of molecular structure models using chime. Bioinformatics 16, 658-659.
11. Thompson, S. E. and Sears, D. W. (2005) Simplifying structure analysis projects with customizable chime-based templates* Biochem. Mol. Biol. Educ. 33, 344-350.
12. Herráez, A. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Educ. 34, 255-261.
13. Cammer, S. (2007) SChiSM2: Creating interactive web page annotations of molecular structure models using Jmol. Bioinformatics 23, 383-384.
14. Gutow, J. H. (2010) Easy Jmol web pages using the Jmol export to web function: A tool for creating interactive web-based instructional resources and student projects with live 3-D images of molecules without writing computer code. J. Chem. Educ. 87, 652-653.
15. Hanson, R. (2010) Jmol-a paradigm shift in crystallographic visualization. J. Appl. Crystallogr. 43, 1250-1260.
16. Hogue, C. W. (1997) Cn3D: A new generation of three-dimensional molecular structure viewer. Trends Biochem. Sci. 22, 314-316.
17. Wang, Y., Geer, L. Y., Chappey, C., Kans, J. A., and Bryant, S. H. (2000) Cn3D: Sequence and structure views for Entrez. Trends Biochem. Sci. 25, 300-302.
18. Porter, S. G., Day, J., McCarty, R. E., Shearn, A., Shingles, R., Fletcher, L., Murphy, S., and Pearlman, R. (2007) Exploring DNA structure with Cn3D. CBE Life Sci. Educ. 6, 65-73.
19. Kaplan, W. and Littlejohn, T. G. (2001) Swiss-PDB viewer (DeepView). Brief Bioinformatics 2, 195-197.
20. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.
21. Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., and Ferrin, T. E. (2006) Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 7, 339.
22. Herráez, A. (2008) How to use Jmol to study and present molecular structures (Vol. 1), Lulu.com, Raleigh, North Carolina.
23. Martz, E. (2002) Protein explorer: Easy yet powerful macromolecular visualization. Trends Biochem. Sci. 27, 107-109.
24. Rhodes, G. (2005) Achieving due recognition for web scholarship: Experience at a structural biology education website. Biochem. Mol. Biol. Educ. 33, 372-374.
25. Craig, P., Bateman, R., and Michel, L. (2011) Survey on educational uses of molecular visualization. Biochem. Mol. Biol. Educ. 39, 3.
26. Craig, P. (2010) Molecular visualization survey. ASBMB Today, December 2010, 2.
27. Prilusky, J., Hodis, E., Canner, D., Decatur, W. A., Oberholser, K., Martz, E., Berchanski, A., Harel, M., and Sussman, J. L. (2011) Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. J. Struct. Biol. 175, 244-252.
28. Krebs, W. G. and Gerstein, M. (2000). Summary and survey. The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28, 1665-1675.
29. Stieff, M., Bateman, R., and Uttal, D. (2005) Teaching and learning with three-dimensional representations in visualization in science education, Gilbert, J., Ed. Springer, Netherlands, pp. 93-120.
30. Schönborn, K. J. and Anderson, T. R. (2008) A model of factors determining students' ability to interpret external representations in biochemistry. Int. J. Sci. Educ. 31, 193-232.
31. Dahmani, H. R., Schneeberger, P., and Kramer, I. M. (2009) Analysis of students' aptitude to provide meaning to images that represent cellular components at the molecular level. CBE Life Sci. Educ. 8, 226-238.
32. Roberts, J. R., Hagedorn, E., Dillenburg, Patrick, M., and Herman, T. (2005) Physical models enhance molecular three-dimensional literacy in an introductory biochemistry course*. Biochem. Mol. Biol. Educ. 33, 105-110.
33. Feig, A. L. and Jabri, E. (2002) Incorporation of bioinformatics exercises into the undergraduate biochemistry curriculum. Biochem. Mol. Biol. Educ. 30, 224-231.
34. Bateman, R. C., Booth, D., Sirochman, R., Richardson, J., and Richardson, D. (2002) Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry. J. Chem. Educ. 79, 551-552.
35. Booth, D., Bateman, R. C., Sirochman, R., Richardson, D. C., Richardson, J. S., Weiner, S. W., Farwell, M., and Putnam-Evans, C. (2005) Assessment of molecular construction in undergraduate biochemistry. J. Chem. Educ. 82, 1854-1858.
36. Bateman, R. C. and Craig, P. A. (2010) A proficiency rubric for biomacromolecular 3D literacy, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Piscataway, NJ. Protein Data Bank Newsletter, pp. 5-7.
37. Richardson, D. C. and Richardson, J. S. (2002) Teaching molecular 3-D literacy. Biochem. Mol. Biol. Educ. 30, 21-26.
38. Schönborn, K. J. and Anderson, T. R. (2006) The importance of visual literacy in the education of biochemists. Biochem. Mol. Biol. Educ. 34, 94-102.
39. Schönborn, K. J. and Anderson, T. R. (2010) Bridging the educational research-teaching practice gap: Foundations for assessing and developing biochemistry students' visual literacy. Biochem. Mol. Biol. Educ. 38, 347-354.
40. Berry, C. and Baker, M. D. (2010) Inside protein structures: Teaching in three dimensions. Biochem. Mol. Biol. Educ. 38, 425-429.
41. Ray, G. B. and Cook, J. W. (2005) Molecular modeling of heme proteins using MOE: Bio-inorganic and structure-function activity for undergraduates*S. Biochem. Mol. Biol. Educ. 33, 194-201.
42. White, B., Kahriman, A., Luberice, L., and Idleh, F. (2010) Evaluation of software for introducing protein structure: Visualization and simulation. Biochem. Mol. Biol. Educ. 38, 284-289.