Curriculum
vitae
David S. Goodsell
Education
University of California at Irvine, B.S. in Chemistry, 1982.
University of California at Irvine, B.S. in Biology, 1982.
University of California at Los Angeles, Ph.D. in Biochemistry, 1987.
Professional Experience
Research and Teaching Assistant, Department of Chemistry and
Biochemistry, University of California at Los Angeles, 1982-1987. Graduate
Advisor: Richard E. Dickerson.
Research Associate, Department of Molecular Biology, Research Institute
of Scripps Clinic, 1987-1990. Postdoctoral Advisor: Arthur J. Olson.
Scientific Associate, Department of Molecular Biology, Research
Institute of Scripps Clinic, 1990-1992. Postdoctoral Advisor: Arthur J. Olson.
Assistant Researcher, Molecular Biology Institute, University of
California at Los Angeles, 1992-1994. Research Director: Richard E. Dickerson.
Assistant Professor, Department of Molecular Biology, The Scripps
Research Institute, 1994-2001.
Associate Professor, Department of Molecular Biology, The Scripps Research
Institute, 2001-2006.
Associate Professor of Molecular Biology, Department of Molecular
Biology, The Scripps Research Institute, 2006-present.
Awards and Honors
Distinguished Teaching Award -- Department of Chemistry and
Biochemistry, University of California at Los Angeles, 1983.
Vesalius Trust Frank Netter Award for Special Contributions to Health
Science Education, 1999, for "The Machinery of Life."
Association of Medical Illustrators Literary Award, 2000, for
"Illustrating the Machinery of Life."
Best Wide Age Appeal Award, SIGKIDS at SIGGRAPH, 2003, for
"Chemystery."
Science and Engineering Visualization Challenge, 2003, National Science
Foundation, Second Place in Illustration, for "Macrophage and Bacterium,
2,000,000X." See Science 301, pg. 1477, 2003.
Art in Crystallography Prize, 2005, American Crystallographic
Association, First Place, for "Blood 2,000,000X."
Sources of Support
Predoctoral Trainee, USPHS National Research Service Award GM-07104,
1983- 1985.
Postdoctoral Fellow, Damon Runyon-Walter Winchell Cancer Research Fund
Fellow DRG 972, 1988-1990.
Co-principal Investigator, "From Atoms to Cells: Multiscale
Computational Integration of Sequence, Structure and Assembly." Department
of Energy, Office of Energy Research, DE-FG03-96EK62272 (Olson PI), 1996-2000.
Co-principal Investigator, "Drug Design Cycle Targeted to
Retroviral Protease." National Institute of General Medical Sciences,
National Institutes of Health, 2P01 GM48870 (Olson PI), 1997-2007.
Principal Investigator, "A Database of General Biomolecular
Information for Education." National Science Foundation, DBI-9904796,
1999-2002.
Co-Principal Investigator, "Tangible Interfaces for Research in
Molecular Biology." National Institutes of Health, R33 EB00798 (Olson PI),
2001-2005.
Co-principal Investigator, "Computer-linked Auto-fabricated Models
for Education in Molecular Biology." National Science Foundation, EIA
0121282 (Olson PI), 2001-2005.
Co-principal Investigator, "A Computational Docking Resource for
Cancer Research." National Institutes of Health, R24 CA95830 (Olson PI),
2002-2007.
Co-principal Investigator, "AutoDock Software Development and
Maintenance." National Institute of General Medical Sciences, National
Institutes of Health, RO1 GM069832 (Olson PI), 2004-2007.
Consultant, "Macromolecular Structure Database." National
Science Foundation, DBI 03-12718 (Berman PI), 2005-2008.
Consortium Principal Investigator, "Using Physical Models to
Enhance Biomolecular Education." National Science Foundation, DUE-0442409
(Herman PI), 2005-2006.
Co-principal Investigator, "Active Learning Modules for the
Molecular Biosciences." National Science Foundation, DUE-0618668 (Herman
PI), 2006-2009.
Professional Activities
Panels and Boards
Special Emphasis Panel, Centers of Biomedical Research Excellence,
National Center for Research Resources, June 18-20, 2000.
Workshop on "Application of Structural Biology in Cancer
Biology," National Cancer Institute, December 11-12, 2000.
Vesalius Trust Board, 2002-present.
National Nanotechnology Initiative Grand Challenge Workshop Series:
Nanotechnology in Space Exploration, NASA, August 24-26, 2004.
Selected Speaking Engagements
Keynote Speaker, "Molecular Graphics: Making Biology
Accessible." Computational Chemistry Conference, C S U Fullerton,
California, January 1994.
Opening Speaker, "Illustration of Macromolecular Size, Shape &
Distribution." Gordon Research Conference on Enzyme Organization and Cell
Function, Oxnard, California, January 1995.
Tutorial, "Bio-Nanotechnology: Lessons from Nature." 7th
Foresight Conference on Molecular Nanotechnology, Santa Clara, California,
October 1999.
Plenary Speaker, "Illustrating the Machinery of Life."
Association of Medical Illustrators Annual Conference (BioComm 2000),
Rochester, Minnesota, July 2000.
Samson Feldman Visiting Scholar in Art as Applied to Medicine, "Art
as Applied to Molecular Medicine." The Johns Hopkins University, School of
Medicine, Baltimore, April 2002.
Invited Speaker, "Exploring the PDB." Symposium on "The
Protein Data Bank in the Classroom and Beyond," ASBMB Annual Meeting,
April 2005.
Plenary Speaker, "Visual Methods from Atoms to Cells." M2Cell
Workshop, Scientific Foundation Fourmentin-Guilbert, Royal Abbey of Fontevraud,
France, December 2005.
Session X Speaker on the Frontiers of Materials Research, "Visual
Methods at the Nanoscale." Materials Research Society Spring Meeting, San
Francisco, April 2006.
Editorial and Curatorial Service
Curator, Molecular Graphics Art Show, Mary and Leigh Block Gallery,
Northwestern University, Chicago. July 7-14, 1994. Held in association with the
13th annual meeting of the Molecular Graphics Society. Catalogue
available at http://www.scripps.edu/pub/goodsell/mgs_art.
Curator, Second Molecular Graphics Art Show, Fleet Space Theatre and
Science Center, San Diego, California. December 1, 1998 to January 15, 1999.
Held in association with the 17th annual meeting of the Molecular
Graphics and Modeling Society. Catalogue available at
http://www.scripps.edu/pub/goodsell/mgs_art.
Editor, Section on Cancer Biology, The Oncologist, Alpha Med Press,
Miamisburg, Ohio, 2002-present.
Editorial Advisory Board, Letters in Drug Design and Discovery, Bentham
Science Publishers, 2003-present.
Consultation
Artistic and Scientific Consultant, Walk-through-cell exhibit. Hall of
Exploration, Columbus Center, Baltimore MD, 1994-1997.
Scientific Consultant, Virtual Explorer. Kent Wilson, Department of
Chemistry, University of California at San Diego, CA, 1995-1997.
Consultant in Bionanotechnology, 2015 Future Threat Technologies Panel,
CIA Headquarters, MD, August 4, 2000.
Scientist-in-Residence, Exploratorium, San Francisco, CA, 2001-2002.
Thinking Partner, NSF Nanoscale Informal Science Education Network,
2005-present.
Interviews
Fenly, L. (2001) Science News: Portraits in Miniature. San Diego Union
Tribune, July 25.
Frankel, F. (2005) Sightings: The Living Cell. American Scientist 93(4),
354-355.
Ghiari, G. (2005) Scienza, Dipingere l'invisibile: Microbi da
Esposizione. Quark 58, 114-118.
Gawrylewski, A. (2007) Molecules, monthly. The Scientist,
http://www.the-scientist.com/news/display/53588.
Panizon, E. (2007) Illustrazione scientifica. Museo della Scienza:
Interattivo e Multimediale, http://immaginarioscientifico.it/is3/archivi/cartoline/set07.html
Honda, T. (2008) Newton, Graphic Science Magazine 2, 42-45.
Bibliography
Books
1. Goodsell, D.S. (1993) "The Machinery of Life"
Springer-Verlag, New York.
2. Goodsell, D.S. (1996) "Our Molecular Nature: The Body's Motors,
Machines and Messages" Springer-Verlag, New York.
3. Goodsell, D.S. (2004) "Bionanotechnology: Lessons from
Nature" Wiley-Liss, Hoboken.
4. Goodsell, D.S. (2009) ÒThe Machinery of Life,Ó Second Edition,
Springer, New York.
Columns
"The Art of Molecular Graphics" in The Journal of Molecular
Graphics and Modelling
1. Gaber, B.P. & Goodsell, D.S. (1997) Irving Geis: Dean of
Molecular Illustrations. Volume 15, 57-59.
2. Goodsell, D.S. & Gaber, B.P. (1998) Color Choices in Molecular Graphics.
Volume 16, 101-103.
3. Goodsell, D.S. (1999) 1998 Molecular Graphics Art Show. Volume 17,
55-56.
4. Goodsell, D.S. & Gaber, B.P. (1999) When Left Isn't Right. Volume
17, 143-144.
5. Goodsell, D.S. & Gaber, B.P. (1999) What Does a Molecule Look
Like? Volume 17, 219-220.
6. Gaber, B.P. & Goodsell, D.S. (1999) Jaggies Begone! Volume 17,
335-336.
7. Goodsell, D.S. & Gaber, B.P. (2000) Escape From Flatland, Volume
18, 71-72.
8. Goodsell, D.S. & Gaber, B.P. (2000) Seeing is Believing, Volume
18, 173-174.
"The Molecular Perspective" in The Oncologist and
Stem Cells
1. Goodsell, D.S. (1999) p53 Tumor Supressor. The Oncologist 4, 138-139;
Stem Cells 17, 189-190.
2. Goodsell, D.S. (1999) The ras Oncogene. The
Oncologist 4, 263-264; Stem Cells 17, 235-236.
3. Goodsell, D.S. (1999)
Methotrexate. The Oncologist 4, 340-341; Stem Cells 17, 314-315.
4. Goodsell, D.S. (1999) The Multidrug Transporter. The Oncologist 4,
428-429; Stem Cells 17, 377-378.
5. Goodsell, D.S. (1999) Matrix Metalloproteinase 2, The Oncologist 4,
509-511; Stem Cells 18, 73-75.
6. Goodsell, D.S. (2000) DNA. The Oncologist 5, 81-82; Stem Cells 18,
148-149.
7. Goodsell, D.S. (2000) Cyclooxygenase-2. The Oncologist 5, 169-171;
Stem Cells 18, 227-229.
8. Goodsell, D.S. (2000) Simian Virus 40. The Oncologist 5, 260-262;
Stem Cells 18, 301-303.
9. Goodsell, D.S. (2000) Microtubules and the Taxanes. The Oncologist 5,
345-346; Stem Cells 18, 382-383.
10. Goodsell, D.S. (2000) Caspases. The Oncologist 5, 435-436; Stem
Cells 18, 457-458.
11. Goodsell, D.S. (2000) The Ribosome. The Oncologist 5, 508-509; Stem
Cells 19, 92-93.
12. Goodsell, D.S. (2001) Targeted Toxins. The Oncologist 6, 110-111;
Stem Cells 19, 161-162.
13. Goodsell, D.S. (2001) Cytochrome P450. The Oncologist 6, 205-206;
Stem Cells 19, 263-264.
14. Goodsell, D.S. (2001) Ultraviolet Light and Pyrimidine Dimers. The
Oncologist 6, 298-299; Stem Cells 19, 348-349.
15. Goodsell, D.S. (2001) Interferons. The Oncologist 6, 374-375; Stem
Cells 19, 467-468.
16. Goodsell, D.S. (2001) The src Oncogene. The Oncologist 6, 474-476;
Stem Cells 19, 553-555.
17. Goodsell, D.S. (2001) Antibodies. The Oncologist 6, 547-548; Stem
Cells 20, 94-95.
18. Goodsell, D.S. (2002) Restriction Endonucleases. The Oncologist 7,
82-83; Stem Cells 20, 190-191.
19. Goodsell, D.S. (2002) Tamoxifen and the Estrogen Receptor. The
Oncologist 7, 163-164; Stem Cells 20, 267-268.
20. Goodsell, D.S. (2002) Bcl-2 and Apoptosis. The Oncologist 7,
259-260; Stem Cells 20, 355-356.
21. Goodsell, D. S. (2002) DNA Topoisomerases. The Oncologist 7,
381-382; Stem Cells 20, 470-471.
22. Goodsell, D. S. (2002) Cadherin. The Oncologist 7, 467-468; Stem
Cells 20, 583-584.
23. Goodsell, D. S. (2002) VEGF and Angiogenesis. The Oncologist 7,
569-570; Stem Cells 21, 118-119.
24. Goodsell, D. S. (2003) Ubiquitin and the Proteosome. The Oncologist
8, 293-294; Stem Cells 21, 509-510.
25. Goodsell, D. S. (2003) Histone Deacetylase. The Oncologist 8,
389-391; Stem Cells 21, 620-621.
26. Goodsell, D. S. (2003) Epidermal Growth Factor. The Oncologist 8,
496-497; Stem Cells 21, 702-703.
27. Goodsell, D. S. (2003) Protein Farnesyltransferase. The Oncologist
8, 597-598; Stem Cells 22, 119-200.
28. Goodsell, D. S. (2004) DNA Polymerase. The Oncologist 9, 108-109;
Stem Cells 22, 236-237.
29. Goodsell, D. S. (2004) Cytochrome c and Apoptosis. The Oncologist 9,
226-227; Stem Cells 22, 428-429.
30. Goodsell, D. S. (2004) Nicotine and Nitrosamines. The Oncologist 9,
353-354; Stem Cells 22, 645-646.
31. Goodsell, D. S. (2004) Polycyclic Aromatic Hydrocarbons. The
Oncologist 9, 469-470; Stem Cells 22, 873-874.
32. Goodsell, D. S. (2004) Cyclins. The Oncologist 9, 592-593; Stem
Cells 22, 1121-1122.
33. Goodsell, D. S. (2004) Morphine. The Oncologist 9, 717-718; Stem
Cells 23, 144-145.
34. Goodsell, D. S. (2005) Major Histocompatibility Complex. The
Oncologist 10, 81-81; Stem Cells 23, 454-455.
35. Goodsell, D. S. (2005) L-Asparaginase. The Oncologist 10, 238-239;
Stem Cells 23, 710-711.
36. Goodsell, D. S. (2005) Double-Stranded DNA Breaks. The Oncologist
10, 361-362; Stem Cells 23, 1021-1022.
37. Goodsell, D. S. (2005) RAD51 and BRCA2. The Oncologist 10, 555-556;
Stem Cells 23, 1434-1435.
38. Goodsell, D. S. (2005) c-Abl Tyrosine Kinase. The Oncologist 10,
758-759; Stem Cells 24, 209-210.
39. Goodsell, D. S. (2006) Tumor Necrosis Factor. The Oncologist 11,
83-84.
40. Goodsell, D. S. (2006) Cisplatin. The Oncologist 11, 316-317; Stem
Cells 24, 514-515.
41. Goodsell, D. S. (2006) Estrogen Sulfotransferase. The Oncologist 11,
418-419.
42. Goodsell, D. S. (2006) Tissue Factor. The Oncologist 11, 849-850.
43. Goodsell, D. S. (2006) Alcohol. The Oncologist 11, 1045-1046.
44. Goodsell, D. S. (2007) Hepatitis B Virus. The Oncologist 12,
516-517.
"Recognition in
Action" in the Journal of Molecular Recognition
1. Goodsell, D. S. (2005) Flipping Pyrimidine Dimers. J. Mol. Recogition
18, 193-195.
2. Goodsell, D. S. (2005) DNA Mimicry. J. Mol. Recognition 18, 427-430.
3. Goodsell, D. S. (2006) Toll-like Receptors. J. Mol. Recognition 19,
387-388.
Book Reviews
1. Goodsell, D. S. (2005) "Into the Nanoworld." Review of
"Soft Machines: Nanotechnology and Life" by Richard A. L. Jones.
American Scientist 93, 183-184.
Internet Publications
1. Goodsell, D.S. (1994-present) Molecular Art|Molecular Science.
Professional WWW Site, http://www.scripps.edu/mb/goodsell.
2. Goodsell, D.S. (1999-present) Molecule of the Month. Protein Data
Bank, http://www.pdb.org. Reprinted in "News and Features" at
Bio.com, http://www.bio.com.
Animated Films
Larsen, T. L., Goodsell, D. S., Meyer, J. C. & Kantardjieff, T. (2001)
"Chemystery." Foundation for Scientific Literacy, San Diego.
Peer-reviewed Scientific Papers
1. Kopka, M.L., Yoon, C., Goodsell, D.S., Pjura, P. & Dickerson,
R.E. (1985) The Molecular Origin of DNA-Drug Specificity in Netropsin and
Distamycin. Proc. Nat. Acad. Sci. USA 82, 1376-1380.
2. Kopka, M.L., Yoon, C., Goodsell, D.S., Pjura, P. & Dickerson,
R.E. (1985) The Binding of an Anti-tumor Drug to DNA: Netropsin and
C-G-C-G-A-A-T-T-BrC-G-C-G. J. Mol. Biol. 183, 553-563.
3. Goodsell, D.S. & Dickerson, R.E. (1986) Isohelical Analysis of
DNA Groove-binding Drugs. J. Med. Chem. 29, 727-733.
4. Dickerson, R.E., Goodsell, D.S., Kopka, M.L. & Pjura, P.E. (1987)
The Effect of Crystal Packing on Oligonucleotide Double Helix Structure. J.
Biomol. Struct. Dynam. 5, 557-579.
5. Goodsell, D.S. (1988) RMS: Programs for Generating Raster Molecular
Surfaces. J. Mol. Graphics 6, 41-44.
6. Yoon, C., Prive, G.G., Goodsell, D.S. & Dickerson, R.E. (1988)
Structure of an Alternating B-DNA Helix and its Relationship to A-tract DNA.
Proc. Natl. Acad. Sci. USA 85, 6332-6336.
7. Goodsell, D.S., Mian, I.S. & Olson, A.J. (1989) Rendering of
Volumetric Data in Molecular Systems. J. Mol. Graphics 7, 41-47.
8. Larsen, T.A., Goodsell, D.S., Cascio, D., Grzeskowiak, K. &
Dickerson, R.E. (1989) The Structure of DAPI Bound to DNA. J. Biomol. Struct.
Dynam. 7, 477-491.
9. Goodsell, D.S. & Olson, A.J. (1990) Automated Docking of
Substrates to Proteins by Simulated Annealing. Proteins: Struct., Funct. &
Genet. 8, 195-202. Includes cover illustration.
10. Olson, A.J. & Goodsell, D.S. (1991) Visualization Blackboard: A
Functional View of Proteins. IEEE Comp. Graph. & Appl. 11(1), 15-17.
11. Goodsell, D.S. (1991) Inside a Living Cell. Trends Biochem. Sci. 16,
203-206. Includes cover illustration.
12. Goodsell, D.S. & Olson, A.J. (1991) Molecular Illustration.
Pixel 2, 36-41. Includes cover illustration.
13. Olson, A.J. & Goodsell, D.S. (1992) Macromolecular Graphics.
Curr. Opinion Struct. Biol. 2, 193-201.
14. Goodsell, D.S. (1992) A Look Inside the Living Cell. Am. Scientist
80(5), 457-465. Includes cover illustration.
15. Olson, A.J. & Goodsell, D.S. (1992) Visualizing Biological
Molecules. Sci. Am. 267(5), 76-81.
16. Goodsell, D.S. & Olson, A.J. (1992) Molecular Illustration in
Black and White. J. Mol. Graphics 10, 235-240
17. Goodsell, D.S., Kopka, M.L., Cascio, D. & Dickerson, R.E. (1993)
Crystal Structure of CATGGCCATG and its Implications for A-Tract Bending
Models. Proc. Natl. Acad. Sci. USA 90, 2930-2934.
18. Goodsell, D.S. & Olson, A.J. (1993) Soluble Proteins: Size,
Shape and Function. Trends Biochem. Sci. 18, 65-68.
19. Goodsell, D.S., Lauble, H., Stout, C.D. & Olson A.J. (1993)
Automated Docking in Crystallography: Analysis of the Substrates of Aconitase.
Proteins: Struct., Funct. & Genet. 17, 1-10. Includes cover illustration.
20. Grzeskowiak, K., Goodsell, D.S., Kaczor-Grzeskowiak, M., Cascio, D.
& Dickerson, R.E. (1993) Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G,
and its Implications for Bending in B-DNA. Biochemistry 32, 8923-8931.
21. Dickerson, R.E., Goodsell, D.S. & Neidle, S.A. (1994)
"...the Tyranny of the Lattice..." Proc. Natl. Acad. Sci. USA 91,
3579-3583.
22. Goodsell, D.S., Kaczor-Grzeskowiak, M. & Dickerson, R.E. (1994)
B-DNA Bending at the T-A Step: The Structure of C-C-A-T-T-A-A-T-G-G. J. Mol.
Biol. 239, 79-96.
23. Goodsell, D.S. & O'Donnell, T.J. (1994) Displays on Display:
Molecular Graphics Art Show. IEEE Comp. Graph. & Appl. 14(6), 5-6.
24. Kopka, M.L., Goodsell, D.S., Baikalov, I., Grzeskowiak, K., Cascio,
D. & Dickerson, R.E. (1994) The Structure of Anthramycin Covalently Bound
to C-C-A-A-C-G-T-T-G- G. Biochem.,
33, 13593-13610.
25. Goodsell, D.S. & Dickerson, R.E. (1994) Bending and Curvature
Calculations in B- DNA. Nucl. Acids Res. 22, 5497-5503.
26. Goodsell, D.S., Grzeskowiak, K. & Dickerson, R.E. (1995) The
Structure of B-helical C-T-C-T-C-G-A-G-A-G: Implications for the Structure of
the Holliday Junction. Biochem 34, 1022-1029.
27. Walker, W.L., Kopka, M.L., Dickerson, R.E. & Goodsell, D.S.
(1995) Design of B- DNA Crosslinking and Sequence-Reading Molecules.
Biopolymers 35, 543-553.
28. Goodsell, D.S., Kopka, M.L. & Dickerson, R.E. (1995) Refinement
of Netropsin Bound to C-G-C-G-A-A-T-T-[brC]-G-C-G: Bias and Feedback in
Crystallographic Refinement. Biochem. 34, 4983-4993.
29. Goodsell, D.S., Larsen T.L. & O'Donnell, T.J. (1995) 1994
Molecular Graphics Art Show and Video Show. J. Mol. Graphics 13, 223-234.
30. Goodsell, D.S., Ng, H.L., Kopka, M.L., Lown, J.W. & Dickerson,
R.E. (1995) Structure of Dicationic Monoimidazole Lexitropsin Bound to DNA.
Biochem. 34, 16654-16661.
31. Morris, G.M., Goodsell, D.S., Huey, R. & Olson A.J. (1996)
Distributed Automated Docking of Flexible Ligands to Proteins: Parallel
Applications of AutoDock 2.4. J. Comp-Aided Mol. Design 10, 293-304.
32. Goodsell, D.S., Morris, G.M. & Olson, A.J. (1996) Automated
Docking of Flexible Ligands: Applications of AutoDock. J. Molec. Recognition 9,
1-5.
33. Dickerson, R.E., Goodsell, D.S. & Kopka, M.L. (1996) MPD and DNA
Bending in Crystals and in Solution. J. Mol. Biol. 256, 108-125.
34. Goodsell, D.S. & O'Donnell, T.J. (1997) Molecular Graphics Art
Show. Leonardo 30, 153-154.
35. Walker, W.L., Kopka, M.L., Dickerson, R.E. & Goodsell, D.S.
(1997) Design of Stapled DNA-Minor-Groove-Binding Molecules with a Mutable Atom
Simulated Annealing Method. J. Comp.-Aided Molec. Design 11, 539-546.
36. Kopka, M.L., Goodsell, D.S., Han, G.W. Chiew, T.K. & Dickerson,
R.E. (1997) Defining GC-Specificity in the Minor Groove: Side-by-side Binding
of a Di- imidazole Lexitropsin to C-A-T-G-G-C-C-A-T-G. Structure 5, 1033-1046.
37. Walker, W.L., Landaw, E.M., Dickerson, R.E. & Goodsell, D.S.
(1997) Estimation of the DNA Sequence Discriminatory Ability of Hairpin-linked
Lexitropsins. Proc. Natl. Acad. Sci. USA 94, 5634-5639.
38. Olson, A.J. & Goodsell, D.S. (1998) Automated Docking and the
Search for HIV Protease Inhibitors. SAR and QSAR in Environmental Research 8,
273-285.
39. Walker, W.L., Landaw, E.M., Dickerson, R.E. & Goodsell, D.S.
(1998) The Theoretical Limits of DNA Sequence Discrimination by Linked
Polyamides. Proc. Natl. Acad. Sci. USA 95, 4315-4320.
40. Larsen, T.A., Olson, A.J. & Goodsell, D.S. (1998) Morphology of
Protein-Protein Interfaces. Structure 6, 421-427.
41. Goodsell, D.S. (1998) Molecules into Cells: Depicting the Cellular
Mesoscale. Leonardo 31, 278
42. Walker, W.L., Kopka, M.L. & Goodsell, D.S. (1998) Progress in
the Design of DNA- Sequence-Specific Lexitropsins. Biopolymers Nucl. Acids 44,
323-334. Includes cover illustration.
43. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E.,
Belew, R.K. & Olson, A.J. (1998) Automated Docking using a Lamarkian
Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comp. Chem.
19, 1639-1662.
44. Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. & Goodsell,
D.S. (1998) Computational Coevolution of Antiviral Drug Resistance. Artificial
Life4, 41-59.
45. Walker, W.L., Goodsell, D.S. & Landaw, E.M. (1998) An Analysis
of a Class of DNA Sequence Reading Molecules. J. Comp. Biol. 5, 571-583.
46. Macke, T.J., Duncan, B.S., Goodsell, D.S. & Olson, A.J. (1998)
Interactive Modeling of Supramolecular Assemblies. J. Mol. Graphics 16,
115-120.
47. Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. & Goodsell,
D.S. (1999) Coevolutionary Analysis of Resistance-Evading HIV-1 Protease
Inhibitors. Proc. Natl. Acad. Sci. USA 96, 1369-1374.
48. Rosin, C.D., Belew, R.K., Walker, W.L., Morris, G.M., Olson, A.J.
& Goodsell, D.S. (1999)
Coevolution and Subsite Decomposition for the Design of Resistance-Evading
HIV-1 Protease Inhibitors. J. Mol. Biol. 287, 77-92.
49. Soares, T.A., Goodsell, D.S., Briggs, J.M., Ferreira, R. &
Olson, A.J. (1999) Docking of 4-Oxalocrotonate Tautomerase Substrates:
Implications for the Catalytic Mechanism. Biopolymers 50, 319-328.
50. Goodsell, D.S. (1999) Where Two World Collide: Art Meets Science.
Chemistry and Industry 9, 348-353.
51. Soares, T., Goodsell, D.S., Ferreira, R., Olson, A.J., Briggs, J.M.
(2000) Ionization State and Molecular Docking Studies for the Macrophage Inhibitory
Factor: the Role of Lysine 32 in the Catalytic Mechanism. J. Molec. Recognition
13, 146-156.
52. Goodsell, D.S. & Olson, A.J. (2000) Structural Symmetry and
Protein Function. Ann. Rev. Biophys. Biomol. Struct. 29, 105-153. Reprinted in:
Biophysics Textbook Online, Supramolecular Assemblies,
http://biosci.umn.edu/biophys/BTOL. Biophysical Society (V. Bloomfield, ed.)
Chapter 14.
53. Goodsell, D.S. (2000) Illustrating the Machinery of Life. J.
Biocommunication 27(4), 12-18.
54. Goodsell, D.S. (2000) Biomolecules and Nanotechnology. Am. Scientist
88, 230-237. Includes cover illustration.
55. Goodsell, D.S. (2001) Sequence Recognition of DNA by Lexitropsins.
Curr. Med. Chem. 8, 509-516.
56. Zhao, S., Goodsell, D.S. & Olson, A.J. (2001) Analysis of a Dataset
of Paired Uncomplexed Protein Structures: New Metrics for Sidechain Flexibility
and Model Evaluation. Proteins: Struct. Funct. & Genet. 43, 271-279.
57. Zhao S., Morris, G.M., Olson, A.J. & Goodsell, D.S. (2001)
Recognition Templates for Predicting Adenylate-binding Sites in Proteins. J.
Mol. Biol. 314, 1245-1255.
58. Osterberg, F., Morris G.M., Sanner, M.F., Olson, A.J. &
Goodsell, D.S. (2002) Automated Docking to Multiple Target Structures:
Incorporation of Protein Mobility and Structural Water Heterogeneity in
AutoDock. Proteins: Struct. Funct. & Genet. 46, 34-40.
59. Goodsell, D.S. (2002) Representation and Misrepresentation in
Biomolecular Science. Theo. Hist. Sci. 6, No. 2, 121-134.
60. Goodsell, D.S. (2002) A Hierarchical Model of HIV-1 Protease Drug
Resistance. Appl. Bioinformatics 1, 3-12.
61. Stoffler, D., Sanner, M.F., Morris, G.M., Olson, A.J. &
Goodsell, D.S. (2002) Evolutionary Analysis of HIV-1 Protease Inhibitors:
Methods for Design of Inhibitors that Evade Resistance. Proteins: Struct. Funct.
Genet. 48, 63-74.
62. Berman, H.M., Goodsell, D.S. & Bourne, P.E. (2002) Protein
Structures: From Famine to Feast. Am. Sci. 90, 350-359. Includes cover
illustration.
63. Yang, P., Craig, P. A., Goodsell, D.S. & Bourne, P.E. (2003)
BioEditor - Simplifying Macromolecular Structure Annotation. Bioinformatics 19,
897-898.
64. Goodsell, D. S. (2003) Looking at Molecules--An Essay on Art and
Science. ChemBioChem 4, 1-5.
65. Rosenfeld, R. J., Goodsell, D. S., Musah, R. A., Morris, G. M.,
Goodin, D. B. & Olson, A. J. (2003) Automated Docking of Ligands to an
Artificial Active Site: Augmenting Crystallographic Analysis with Computer
Modeling. J. Comp. Aided Mol. Design 17, 525-536.
66. Brik, A., Muldoon, J., Lin, Y.-C., Elder, J.H., Goodsell, D.S.,
Olson, A. J., Fokin, V. V., Sharpless, K. B. and Wong, C.-H. (2003) Rapid
Diversity-Oriented Synthesis in Microtiter Plates for In Situ Screening of HIV
Protease Inhibitors. ChemBioChem 4, 1246-1248.
67. Huey, R., Goodsell, D. S., Morris, G. M. & Olson, A. J. (2004) Grid-Based
Hydrogen Bond Potentials with Improved Directionality. Letters Drug Design
Discovery 1, 88-93.
68. Goodsell, D. S. (2005)
Visual Methods from Atoms to Cells. Structure 13, 347-354.
69. Berman, H. M., Ten Eyck, L. F., Goodsell, D. S., Haste, N. M.,
Kornev, A. & Taylor, S. S. (2005) The cAMP Binding Domain: An Ancient
Signaling Module. Proc. Natl. Acad. Sci. USA 102, 45-40.
70. Cheng, T.-J., Goodsell, D. S. & Kan, C.-C. (2005) Identification
of Sanguinarine as a Novel HIV Protease Inhibitor from in Vivo High-Throughput
Screening of 2,000 Drugs and Natural Products with a Cell-based Assay. Letters
Drug Design Discovery 2, 364-371.
71. Brik, A., Alexandros, J., Lin, Y.-C., Elder, J.H., Olson, A.J.,
Wlodawer, A., Goodsell, D.S. & Wong, C.-H. (2005) 1,2,3-Triazole as a
Peptide Surrogate in the Rapid Synthesis of HIV Protease Inhibitors.
ChemBioChem 6, 1167-1169.
72. Beuscher, A., Olson, A. J. & Goodsell, D. S. (2005) Identifying
Protein Binding Sites and Optimal Ligands. Letters Drug Design Discovery 2, 483-489.
73. Goodsell, D. S. (2006) Seeing the Nanoscale. NanoToday 1(3), 44-49.
74. Herman, T., Morris, J., Colton, S., Batiza, A., Patrick, M.,
Franzen, M. & Goodsell, D. S. (2006) Tactile Teaching: Exploring Protein
Structure/Function Using Physical Models. Biochem. Mol. Biol. Education
(BAMBED) 34, 247-254.
75. Huey, R., Morris, G. M., Olson, A. J. & Goodsell, D. S. (2007) A
Semi-empirical Free Energy Force Field with Charge-based Desolvation. J. Comp.
Chem. 28, 1145-1152.
76. Goodsell, D. S. (2007) Making the Step from Chemistry to Biology and
Back. Nature Chem. Biol. 3, 681-684.
77. Harris, R., Olson, A. J. & Goodsell, D. S. (2007) Automated
Prediction of Ligand-Binding Sites in Proteins. Proteins Struct. Funct. Bioinf.
70, 1506-1517.
78. Goodsell, D. S. & Johnson, G. T. (2007) Filling the Gaps:
Artistic License in Education and Outreach. PLoS Biology 5:12, 2759-2762.
79. Chang, M. W., Belew, R. K., Carroll, K. S., Olson, A. J. &
Goodsell, D. S. (2008) Empirical Entropic Contributions in Computational Docking:
Evaluation in APS Reductase Complexes. J. Comput. Chem. 29, 1753-1761.
80. Cosconati, S., Hong, J. A., Novellino, E., Carroll, K. S., Goodsell,
D. S. & Olson, A. J. (2008) Structure-Based Virtual Screening and
Biological Evaluation of Mycobacterium tuberculosis Adenosine 5Õ-Phosphosulfate
Reductase Inhibitors. J. Med. Chem. 51, 6627-6630.
81. Goodsell, D. S. (2009) Fact and Fantasy in Nanotech Imagery.
Leonardo 42, 52-57.
82. Goodsell, D. S. (2009) Illustrating the Machinery of Life:
Neuromuscular Synapse. Biochem. Mol. Biol. Education 37, 204-210.
83. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K.,
Goodsell, D. S. & Olson, A. J. (2009) AutoDock4 and AutoDockTools4:
Automated Docking with Selective Receptor Flexibility. J. Comp. Chem. 30,
2785-2791.
84. Goodsell, D. S. (2009) Illustrating the Machinery of Life:
Escherichia coli. Biochem. Mol. Biol. Education 37, 325-332.
85. Goodsell, D. S. & Klionsky, D. J. (2010) Artophagy: The Art of
AutophagyÑThe CVT Pathway. Autophagy 6, 3-6.
86. OÕDonoghue, S. I., Gavin, A.-C., Gehlenborg, N., Goodsell, D. S.,
Heriche, J.-K., Nielsen, C. B., North, C., Olson, A. J., Procter, J. B.,
Shattuck, D. W., Walter, T. & Wong, B. (2010) Visualizing Biological
DataÑNow and in the Future. Nature Methods 7, S2-S4.
87. OÕDonoghue, S. I., Goodsell, D. S., Frangakis, A. S., Jossinet, F.,
Laskowski, R. A., Nilges, M., Saibil, H. R., Schafferhans, A., Wade, R. C.,
Westhof, E. & Olson, A. J. (2010) Visualization of Macromolecular
Structures. Nature Methods 7, S42-S55.
Peer-Reviewed Scientific
Papers in Press
n/a
Symposium Proceedings and Book Chapters
1. Kopka, M.L., Pjura, P., Yoon, C., Goodsell, D.S. & Dickerson,
R.E. (1985) The Binding of Netropsin to Double-Helical B-DNA of Sequence
C-G-C-G-A-A-T-T-BrC-G-C-G: Single Crystal X-Ray Structure Analysis. In
Structure and Motion: Membranes, Nucleic Acids and Proteins (E. Clementi, G.
Corongiu, M.H. Sarma & R. Sarma, eds.) Adenine Press, New York, pp.
461-483. Includes cover illustration.
2. Dickerson, R.E., Pjura, P., Kopka, M.L., Goodsell, D.S. & Yoon,
C. (1985) Rational Design of DNA Minor Groove-Binding Anti-Tumor Drugs. In
Crystallography in Molecular Biology, Proceedings of the NATO Advanced Study
Institute and EMBO Lecture Course, Bischenberg, Alsace, France, September 1985.
NATO ASI Series (D. Moras, ed.) Plenum, New York, pp. 209-221.
3. Eisenberg, D., Wesson, M., Goodsell, D.S., Wilcox, W., Gribskov, M.,
Altschuh, D. & Rees, D.C. (1987) Solvation Energy Contributions to Binding
Energies. In Protein Structure, Folding and Design 2, Alan R. Liss, pp 203-213.
4. Kopka, M.L., Pjura, P.E., Goodsell, D.S. & Dickerson, R.E. (1987)
Drugs and Minor Groove Binding in DNA: Netropsin and Hoeschst 33258. In Nucleic
Acids and Molecular Biology, Springer Verlag, Berlin, pp 1-24.
5. Goodsell, D.S. & Olson, A.J. (1989) Molecular Applications of
Volume Rendering and 3-D Texture Maps. In Proceedings of the Volume
Visualization Workshop, Chapel Hill, NC, May 1989. Department of Computer
Science, University of North Carolina, Chapel Hill, NC, pp 27-31. Includes
cover illustration.
6. Goodsell, D.S. & Olson, A.J. (1990) Rendering Volumetric Data in
Biological Systems. In Bioimaging and Two-Dimensional Spectroscopy (L.C. Smith,
ed.) Proc. SPIE 1205, pp. 117-124.
7. Goodsell, D.S., Grzeskowiak, K., Kopka, M.L. & Dickerson, R.E.
(1994) Base Pair Roll and Tilt in B-DNA Bending. In Structural Biology: State
of the Art (R.H. Sarma & M.H.Sarma, eds.) Adenine Press, New York, pp.
215-220.
8. Goodsell, D.S. (1995) Molecules in Living Cells. In Principles of
Medical Biology, Vol. 3: Cellular Organelles and the Extracellular Matrix
(Bittar & Bittar, eds.) JAI Press, Greenwich, CT, pp. 173-180.
9. Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. & Goodsell,
D.S. (1998) Computational Coevolution of Antiviral Drug Resistance. In
Proceedings of the Sixth International Conference on Artificial Life (C. Adami,
R.K. Belew, H. Kitano & C.E. Taylor, eds.) MIT Press, Cambridge, pp. 81-90.
10. Goodsell, D.S. (1999) Atomistic vs. Continuous Representations in
Molecular Biology. In Visual Representations and Interpretations (R. Paton and
I. Nelson, eds.) Springer Verlag, London, pp. 146-155.
11. Walker, W.L., Goodsell, D.S., Dickerson, R.E. & Landaw, E.M.
(1999) A Preliminary Multiobjective Analysis of the Chemotherapeutic Benefits
of Hairpin-Linked Polyamides. In Rational Drug Design, The IMA Volumes in
Mathematics and Its Applications.
(D.G. Truhlar, W. J. Howe, A. J. Hopfinger, J. Blaney & R. A.
Dammkoehler, eds.) Springer Verlag, New York, pp. 81-92.
12. Morris, G.M., Olson, A.J. & Goodsell, D.S. (2000) Protein-Ligand Docking. In Evolutionary
Algorithms in Molecular Design (D.E. Clark, ed.) Wiley-VCH, Weinheim, Germany,
pp. 31-48.
13. Goodsell, D.S. (2003) Illustrating Molecules. In The Guild Handbook
of Scientific Illustration, Second Edition (E.R.S. Hodges, ed.) Chapter 15, pp.
267-270. J. Wiley and Sons, New Jersey.
14. Gillet, A., Sanner, M., Stoffler, D., Goodsell, D. S. and Olson, A.
J. (2004) Augmented Reality with Tangible Auto-fabricated Models for Molecular
Biology Applications. In Proceedings of the IEEE Visualization 2004, IEEE
Computer Society, Washington, DC, pp 235-242.
15. Gillet, A., Goodsell, D., Sanner, M. F., Stoffler, D. & Olson,
A. J. (2004) Computer-linked Autofabricated 3D Models for Teaching Structural
Biology. In Proceedings of SIGGRAPH 2004, Association for Computing Machinery.
16. Goodsell, D.S. (2005) Computational Docking of Biomolecular
Complexes with AutoDock. In Protein-Protein Interactions, A Molecular Cloning
Manual, Second Edition (E. A. Golemis and P. D. Adams, ed.). Cold Spring Harbor
Laboratory Press, New York, pp 885-892.
17. Goodsell, D.S. (2005) Representing Structural Information. Current
Protocols in Bioinformatics, J. Wiley and Sons, Hoboken, New Jersey, pp 5.4.1-5.4.23.
Original Art and
Illustration
1. Goodsell, D.S. & Curlender, D. (1984) Two illustrations. In
Johnston, R. "Light Relief" Vogue 141, 120-122.
2. Goodsell, D.S. & Curlender, D. (1985) "The Dancer"
& "Larger Than Life" In Picture Gallery; Lead illustration in Art
and Animation. IEEE Comp. Graph. & Appl. 5, 10- 12, 31.
3. Goodsell, D.S. (1986) Cover illustration. UCLA Med. 9.
4. Goodsell, D.S. & Olson, A.J. (1989) Cover illustration. Comm. ACM
32, No. 4.
5. Goodsell, D.S. & Olson, A.J. (1989) Technical Slide 73, Stereo
Slides 1+2, 5+6, 7+8, 9+10. SIGGRAPH 1989 Slide Sets.
6. Goodsell, D.S. & Olson, A.J. (1990) Technical Slide 41. SIGGRAPH
1990 Slide Set.
7. Goodsell, D.S. (1991) Technical Slide 74, Stereo Slide 9+10. SIGGRAPH
1991 Slide Sets.
8. Goodsell, D.S. (1992) "Intimacies" (color photocopy). Shown
at SIGGRAPH 1992 Art Show. Slide 23, SIGGRAPH 1992 Art Show Slide Set.
Collection of Ellen Sandor.
9. Goodsell, D.S. (1992) Technical Slide 14. SIGGRAPH 1992 Slide Sets.
10. Goodsell, D.S. (1994) Cover illustration. In Scopes, R.K.
"Protein Purification" Springer-Verlag, New York.
11. Goodsell, D.S. (1994) "Inside a Eukaryotic Cell" (picture
essay) & "Picturing Biochemistry" (cover illustration) In Moran,
L.A. & Scrimgeour, K.G. "Biochemistry" Neil Patterson
Publishers/Prentice Hall, North Carolina. "Picturing Biochemistry"
shown at Molecular Graphics Art Show, Block Gallery, Northwestern University,
Chicago, July 1994. Picturing Biochemisty, collection of T. J. O'Donnell.
12. Goodsell, D.S. (1997) "Cytoplasm with Small Molecules,
2,000,000X." In Guttman, B. & Hopkins, J. "Biology" W.C.
Brown Communications, Dubuque, Iowa. Collection of Linda Nye.
13. Goodsell. D.S. (1998) "Immune Recognition" (cover
illustration). In "1996-1997 Scientific Report" of the Scripps
Research Institute, La Jolla, California. Shown in HMSBeagle
(http://www.biomednet.com/hmsbeagle) Art Gallery, Issue 72, February 2000.
Reprinted in "Art and Medicine: Art at the Molecular Level" Heart
Views 1, 284 (2000); Betts, M. (2004) "The Human Body" Walker &
Company, New York. Collection of Lucy Pawlak.
14. Goodsell, D.S. (1999) "Prokaryotic Compartmentation" and
"Cellulosome." In Hoppert, M. and Mayer, F. "Prokaryotes"
Am. Scientist. 87, 518-525. Reprinted in: Prescott, L.M, Harley, J.P. &
Klein D.A. "Microbiology" McGraw-Hill, New York, 2002; Hapgood, F.
(2003) "A Microbe Enters the Matrix" Wired 9, 42; Dobson, C. M.
(2004) "Crossing the Boundary" Nature 432, 444-445; Pielak, G. J.
(2005) "A Model of Intracellular Organization" Proc. Natl. Acad. Sci.
USA 102, 5001-2002; Szilagyi, A., Grimm, V., Arakaki, A.K. & Skolnick, J.
(2005) "Prediction of Physical Protein-Protein Interaction" Phys.
Biol. 2, S1-S16. Collection of Michelle Hoffman and Linda Huff, respectively.
15. Goodsell, D.S. (2000) "Nuclear Pore Complex" (cover
illustration). In Cooper, G.M. "The Cell: A Molecular Approach" ASM
Press/Sinauer Associates, Sunderland, Mass.
16. Goodsell, D.S. (2002) "Macrophage and Bacterium
2,000,000X." Commission for the Center of Integrative Molecular
Biosciences, Scripps Research Institute, La Jolla, California. Cover
illustration for National Science Foundation FY2005 Summary of Budget Request
to Congress.
17. Goodsell, D.S. (2003) "How Does a Muscle Work?" Mark
McGowan, graphic designer. Poster in the Exploratorium Quarterly, Winter 2003.
Honorable Mention for Informational Graphics in the 2007 National Science
Foundation Visualization Challenge, Science 317, 1857-1863 (2007).
18. Goodsell, D.S. (2005) "Erythropoietin" (journal
illustration). In Ritter, S. "Erythropoietin" Chemical and
Engineering News Vol. 83, No. 25, Pg. 64.
19. Goodsell, D.S. and Johnson, G. (2005) "Biopolis."
Commission in seven panels for Biopolis, Singapore.
20. Goodsell, D.S. (2005) "Biosites." Commission in six panels
for Biosite, San Diego.
21. Goodsell, D. S. (2006) "Autophagy." Commission for Dan
Klionsky, University of Michigan, Ann Arbor. Cover illustration for the Journal
of Cell Biology, Volume 175(6), 2006.
22. Goodsell, D. S. (2006) "Hematopoiesis." Commission for Kenneth
Kaushansky, University of California, San Diego.
23. Goodsell, D. S. (2006) Illustrations for Renneberg, R.
"Biotechnologie fur Einsteiger" Elsevier, Munich.
24. Goodsell, D. S. (2007) Illustrations for "Inside DNA," a
traveling exhibition from At-Bristol, Bristol, UK.
Showing of Artwork
Group Show. Annual Meeting of the Guild of Natural Science Illustrators.
Richland, Washington. August 7-13, 1999.
Group Show. "Image and Meaning: Envisioning and Communicating
Science and Technology." Massachusetts Institute of Technology. June
13-16, 2001.
Group Show. "The Art of Science - Images from the Protein Data
Bank." The Gallery, Rutgers University, New Jersey. January-February,
2002. Currently traveling.
Feature Exhibit. 57th Annual Meeting of the Association of
Medical Illustrators. Austin, Texas. July 24-28, 2002.
Group Show. "Art of Science." Atrium Gallery, California State
University at Fullerton, October-December 2003.
Group Show. "The Beauty of Phenomena: Art in the Communication of
Science." National Academy of Sciences, Washington, D.C., April-September
2003. New York Hall of Science, Queens, New York, December 2003-March 2004.
Fresno Museum of Art, History and Science, Fresno, California, July-October
2004.
Group Show. "Annual Members Exhibition of the Guild of Natural
Science Illustrators." Jacobs Gallery, Hult Center for the Performing
Arts, Eugene, Oregon, June-July 2005.
Group Show. "The Visual Communication of Science." Sunderland
Museum and Winter Gardens, Sunderland, UK, September-October 2007; MISM,
Manchester, UK, November-December 2007; Nobel Museum, Stockholm, Sweden,
February-June 2008. Catalogue: Wheeler, S. and Long, A. "Design4Science:
the Visual Communication of Science," Gmelin Press and the University of
Sunderland, 2007.