Visualization software for molecular assemblies.

Thomas D Goddard, Thomas E Ferrin
Author Information
  1. Thomas D Goddard: Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158-2517, USA.

Abstract

Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments, and other molecular assemblies is advancing on many fronts. New developments include molecular representations that offer better control over level of detail, lighting that improves the perception of depth, and two-dimensional projections that simplify data interpretation. Programmable graphics processors offer quality, speed, and visual effects not previously possible, while 3D printers, haptic interaction devices, and auto-stereo displays show promise in more naturally engaging our senses. Visualization methods are developed by diverse groups of researchers with differing goals: experimental biologists, database developers, computer scientists, and package developers. We survey recent developments and problems faced by the developer community in bringing innovative visualization methods into widespread use.

References

  1. Structure. 2005 Mar;13(3):483-91 [PMID: 15766549]
  2. J Mol Graph Model. 1998 Jun;16(3):115-20, 162-3 [PMID: 10434250]
  3. Structure. 2005 Mar;13(3):347-54 [PMID: 15766535]
  4. Nucleic Acids Res. 2000 Jan 1;28(1):235-42 [PMID: 10592235]
  5. Structure. 2005 Mar;13(3):381-8 [PMID: 15766539]
  6. Methods Enzymol. 1997;277:571-90 [PMID: 18488325]
  7. J Struct Biol. 2007 May;158(2):205-13 [PMID: 17400476]
  8. J Struct Biol. 2007 Jan;157(1):271-80 [PMID: 17029847]
  9. IEEE Trans Image Process. 2005 Sep;14(9):1324-37 [PMID: 16190468]
  10. IEEE Trans Vis Comput Graph. 2006 Sep-Oct;12(5):1237-44 [PMID: 17080857]
  11. Trends Biochem Sci. 1998 Sep;23(9):358-61 [PMID: 9787643]
  12. J Comput Chem. 2004 Oct;25(13):1605-12 [PMID: 15264254]
  13. Structure. 2005 Mar;13(3):473-82 [PMID: 15766548]
  14. Structure. 2005 Mar;13(3):447-62 [PMID: 15766546]
  15. Bioinformatics. 2003 Jan 22;19(2):311-2 [PMID: 12538265]
  16. Nat Struct Mol Biol. 2007 May;14(5):354; discussion 354-5 [PMID: 17473875]
  17. J Struct Biol. 2005 Aug;151(2):196-207 [PMID: 16043364]
  18. PLoS Comput Biol. 2006 Nov 17;2(11):e155 [PMID: 17112313]
  19. J Mol Graph. 1996 Feb;14(1):33-8, 27-8 [PMID: 8744570]
  20. J Struct Biol. 2007 Jan;157(1):38-46 [PMID: 16859925]
  21. J Struct Biol. 2003 Oct-Nov;144(1-2):123-31 [PMID: 14643215]
  22. Trends Biochem Sci. 2002 Nov;27(11):589 [PMID: 12417136]
  23. BMC Bioinformatics. 2002;3:2 [PMID: 11869452]
  24. J Mol Biol. 1995 Apr 7;247(4):536-40 [PMID: 7723011]
  25. J Exp Psychol. 1953 Apr;45(4):205-17 [PMID: 13052853]
  26. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D386-9 [PMID: 16381893]
  27. Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 [PMID: 15299374]
  28. J Mol Graph Model. 2006 Nov;25(3):380-8 [PMID: 16563824]
  29. Nucleic Acids Res. 2006;34(4):e29 [PMID: 16478715]
  30. Biochem Mol Biol Educ. 2006 Jul;34(4):247-54 [PMID: 21638686]
  31. J Struct Biol. 2007 Jan;157(1):262-70 [PMID: 17070699]
  32. J Struct Biol. 2007 May;158(2):182-7 [PMID: 17116403]

Grants

  1. P41 RR001081/NCRR NIH HHS
  2. P41 RR001081-30/NCRR NIH HHS
  3. P41RR01081/NCRR NIH HHS

MeSH Term

Computer Simulation
Macromolecular Substances
Models, Molecular
Molecular Conformation
Nucleic Acids
Proteins
Ribosomes
Software
Viruses

Chemicals

Macromolecular Substances
Nucleic Acids
Proteins

Word Cloud

Created with Highcharts 10.0.0molecularassembliesdevelopmentsofferVisualizationmethodsdevelopersSoftwareviewingthree-dimensionalmodelsmapsvirusesribosomesfilamentsadvancingmanyfrontsNewincluderepresentationsbettercontrolleveldetaillightingimprovesperceptiondepthtwo-dimensionalprojectionssimplifydatainterpretationProgrammablegraphicsprocessorsqualityspeedvisualeffectspreviouslypossible3Dprintershapticinteractiondevicesauto-stereodisplaysshowpromisenaturallyengagingsensesdevelopeddiversegroupsresearchersdifferinggoals:experimentalbiologistsdatabasecomputerscientistspackagesurveyrecentproblemsfaceddevelopercommunitybringinginnovativevisualizationwidespreadusesoftware

Similar Articles

Cited By