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 of Molecular Biology, The Scripps Research Institute, 1994-2001.

Associate Professor of Molecular Biology, The Scripps Research Institute, 2001-present.

 

Awards and Honors

Distinguished Teaching Award -- Department of Chemistry and Biochemistry, University of California at Los Angeles, 1983.

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.

Vesalius Trust Frank Netter Award for Special Contributions to Health Science Education, 1999, for "The Machinery of Life."

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, 1996-2000.

Co-principal Investigator, "Drug Design Cycle Targeted to Retroviral Protease."  Structural Biology of Aids-related Proteins, National Institute of General Medical Sciences, National Institutes of Health, 2P01 GM48870, 1997-present.

Principal Investigator, "A Database of General Biomolecular Information for Education." Database Activities in Biological Science, Division of Biological Infrastructure, National Science Foundation, DBI-9904796, 1999-2002.

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.

Co-principal Investigator, "Using Physical Models to Enhance Biomolecular Education."  Educational Materials Development Program, Division of Course, Curriculum and Laboratory Improvement, National Science Foundation, 2005-present.

Art in Crystallography Prize, 2005, American Crystallographic Association, First Place, for "Blood 2,000,000X."

 

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.

 

Invited 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.

 

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.

 

Membership in Scholarly Societies

American Crystallographic Association

American Association for the Advancement of Science

International Society for the Arts, Sciences and Technology

Guild of Natural Science Illustrators

Association of Medical Illustrators

 

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.

 

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.

 

Animated Films

Larsen, T. L., Goodsell, D. S., Meyer, J. C. & Kantardjieff, T. (2001) "Chemystery." Foundation for Scientific Literacy, San Diego.

 

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.

 

Internet Publications

1. Goodsell, D.S. (1994-present) Molecular Art|Molecular Science. Professional WWW Site, http://www.scripps.edu/pub/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.

 

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.

 

Peer-Reviewed Scientific Papers in Press

XX. Brik, A., Alexandros, J., Lin, Y.-C., Elder, J.H., Olson, A.J., Wlodawer, A., Goodsell, D.S. & Wong, C.-H. (200-) 1,2,3-Triazole as a Peptide Surrogate in the Rapid Synthesis of HIV Protease Inhibitors. ChemBioChem, in press.

XX. Beuscher, A., Olson, A. J. & Goodsell, D. S. (200-) Identifying Protein Binding Sites and Optimal Ligands. Letters Drug Design Discovery, in press.

 

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. 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.

16. 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.

 

Symposium Proceedings and Book Chapters in Press

n/a

 

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. (2005) "Erythropoietin" (journal illustration). In Ritter, S. "Erythropoietin" Chemical and Engineering News Vol. 83, No. 25, Pg. 64.

 

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.

 

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.