David Goodsell, JR, PhD
Scripps Research Joint Appointments
Other Joint Appointments
Center for Integrative Proteomics Research, Rutgers State University of New JerseyRCSB Protein Data Bank
Research Focus
Computer graphics and simulation are used to study structure/function relationships in key biological systems. Current projects include modeling the molecular structure of entire cells and development of AutoDock, our general computational docking method. Science outreach is also a strong focus of the lab, with projects such as the "Molecule of the Month," a feature at the RCSB Protein Data Bank that presents the structure and function of a new molecule each month, creation of HIV-related materials for the B-HIVE Center, and several illustrated books on biological molecules, their diverse roles within living cells, and the growing connections between biology and nanotechnology.
Education
Ph.D. (Biochemistry), University of California, Los Angeles, 1987B.S. (Biology), University of California, Irvine, 1982
B.S. (Chemistry), University of California, Irvine, 1982
Professional Experience
2013-2020 Associate Professor of Molecular Biology, Integrative Structural and Computational Biology (ISCB), Scripps Research2006-2012 Associate Professor of Molecular Biology, Molecular Biology, Scripps Research
2001-2006 Associate Professor, Molecular Biology, Scripps Research
1994-2001 Assistant Professor, Molecular Biology, Scripps Research
1992-1994 Assistant Researcher, Molecular Biology Institute, University of California, Los Angeles
1990-1992 Scientific Associate, Department of Molecular Biology, Research Institute of Scripps Clinic
1987-1990 Research Associate, Department of Molecular Biology, Research Institute of Scripps Clinic
Awards & Professional Activities
Vesalius Trust Frank Netter Award for Special Contributions to Health Science Education, 1999Association of Medical Illustrators Literary Award, 2000
Overall Winner, Wellcome Image Awards, 2016
Fankuchin Memorial Award, American Crystallographic Association, 2022
Carl Branden Award, Protein Society, 2022
Selected References
My Bibliography at the National Library of Medicine: https://www.ncbi.nlm.nih.gov/sites/myncbi/1DC2wYciwsuQd/bibliography/44254495/public/?sort=date&direction=descending
Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. & Goodsell, D.S. Coevolutionary Analysis of Resistance-Evading HIV-1 Protease Inhibitors. Proc. Natl. Acad. Sci. USA 96, 1369-1374, 1999.
Goodsell, D.S. & Olson, A.J. Structural Symmetry and Protein Function. Ann. Rev. Biophys. Biomol. Struct. 29, 105-153, 2000.
Goodsell, D.S. Biomolecules and Nanotechnology. Am. Scientist 88, 230-237, 2000.
Zhao S., Morris, G.M., Olson, A.J. & Goodsell, D.S. Recognition Templates for Predicting Adenylate-binding Sites in Proteins. J. Mol. Biol. 314, 1245-1255, 2001.
Goodsell, D. S. (2005) Visual Methods from Atoms to Cells. Structure 13, 347-354.
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.
Goodsell, D. S. (2007) Making the Step from Chemistry to Biology and Back. Nature Chem. Biol. 3, 681-684.
Harris, R., Olson, A. J. & Goodsell, D. S. (2007) Automated Prediction of Ligand-Binding Sites in Proteins. Proteins Struct. Funct. Bioinf. 70, 1506-1517.
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.
Goodsell, D. S. (2009) Illustrating the Machinery of Life: Escherichia coli. Biochem. Mol. Biol. Education 37, 325-332.
Goodsell, D. S. (2010) Illustrating the Machinery of Life: Mitochondrion Biochem. Mol. Biol. Education 38, 134-140.
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.
Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D.S. & Olson, A.J. (2010) Virtual Screening with AutoDock: theory and practice. Expert Opinion in Drug Discovery 5, 597-607.
O'Donoghue, 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
Dutta, S., Zardecki, C., Goodsell, D. S. & Berman, H. M. (2010) Promoting a Structure View of Biology for Varied Audiences: An Overview of RCSB PDB Resources and Experiences. J. Appl. Cryst. 43(5), 1224-1229.
Goodsell, D. S. (2010) The Protein Data Bank: Exploring Biomolecular Structure. Nature Education 3(9): 39.
Goodsell, D. S. (2011) Illustrating the Machinery of Life: Eukaryotic Cell Panorama. Biochem. Mol. Biol. Education 39, 91-101.
Johnson, G.T., Autin, L., Goodsell. D. S., Sanner, M. F. & Olson, A. J. (2011) ePMV Embeds Molecular Modeling into Professional Animation Software Environments. Structure 19, 293-303.
Leonard, S. E., Garcia, F. J., Goodsell, D. S. & Carroll, K. S. (2011) Redox-based Probes for Protein Tyrosine Phosphatases. Angew. Chem. Int. Ed. 50, 4423-4427.
Cosconati, S., Marinella, L., Di Leva, F. S., La Pietra, V., De Simone, A., Mancini, F., Andrisano, V., Novellino, E., Goodsell, D. S. & Olson, A. J. (2012) Protein Flexibility in Virtual Screening: The BACE-1 Case Study. J. Chem. Inf. Model. 52, 2697-2704.
Goodsell, D. S. (2012) Illustrating the Machinery of Life: Viruses. Biochem. Mol. Biol. Education 40, 291-296.
Goodsell, D. S. (2012) Putting Proteins in Context. Bioessays 34, 718-720.
Batiza, A. F., Gruhl, M., Zhang, B., Harrington, T., Roberts, M., LaFlamme, D., Haasch, M. A., Knopp, J.M., Vogt, G., Goodsell, D., Hagedorn, E., Marcey, D., Hoelzer, M. & Nelson, D. (2013) The effects of the SUN project on teacher knowledge and self-efficacy regarding biological energy transfer are significant and long-lasting: results of a randomized controlled trial. CBE-Life Science Education 12, 287-305.
Span, E. A., Goodsell, D. S., Ramchandran, R., Franzen, M. A., Herman, T. & Sem, D. S. (2013) Protein structure in context: the molecular landscape of angiogenesis. Biochem. Mol. Biol. Education 41, 213-223.
Goodsell, D. S., Burley, S. K. & Berman, H. M. (2013) Revealing structural views of biology. Biopolymers 99, 817-824.
Johnson, G. T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M. F. & Olson, A. J. (2014) 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discuss. DOI 10.1039/c4fd00017j.
Rose, P. W., Prlic, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J. D., Woo, J., Young, J., Zardecki, C., Berman, H. M., Bourne, P. E. & Burley, S. K. (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Research 43, D345-D356. Doi 10.1093/nar/gku1214.
Goodsell, D. S., Dutta, S., Zardecki, C., Voigt, M., Berman, H. M. & Burley, S. K. (2015) The RCSB PDB "Molecule of the Month": Inspiring a molecular view of biology. PLoS Biology 13(5), e1002140. DOI:10.1371/journal.pbio.1002140.
Goodsell, D. S. (2015) Illustrations of the HIV life cycle. Curr. Top. Microbiol. Immunol. 389, 243-252.
Johnson, G. T., Autin, L., Al-Alusi, M. Goodsell, D. S., Sanner, M. F. & Olson, A. J. (2015) cellPACK: A virtual mesoscope to model and visualize structural systems biology. Nat. Methods 12, 85-91.
Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J. & Sanner, M. F. (2015) AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS Computational Biology 11(12), e1004586. DOI:10.1371/journal.pcbi/1004586.
Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S. & Olson, A. J. (2016) Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat. Protocols 11, 905-919.
Goodsell, D. S. (2016) Cellular Landscapes in Watercolor. J. Biocommunication 40, 22-26.
Links
Molecular Art | Molecular Science: Home of David S. Goodsell