• 28195 Citations
  • 47 h-Index
1985 …2021

Research output per year

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Research Output

2020

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Goodsell, D. S., Zardecki, C., Di Costanzo, L., Duarte, J. M., Hudson, B. P., Persikova, I., Segura, J., Shao, C., Voigt, M., Westbrook, J. D., Young, J. Y. & Burley, S. K., Jan 1 2020, In : Protein Science. 29, 1, p. 52-65 14 p.

Research output: Contribution to journalReview article

1 Scopus citations
2019

Cuttlefish: Color Mapping for Dynamic Multi-Scale Visualizations

Waldin, N., Waldner, M., Le Muzic, M., Gröller, E., Goodsell, D. S., Autin, L., Olson, A. J. & Viola, I., Sep 1 2019, In : Computer Graphics Forum. 38, 6, p. 150-164 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Illustrate: Software for Biomolecular Illustration

Goodsell, D. S., Autin, L. & Olson, A. J., Nov 5 2019, In : Structure. 27, 11, p. 1716-1720.e1

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Integrative modeling of the HIV-1 ribonucleoprotein complex

Goodsell, D. S., Jewett, A., Olson, A. J. & Forli, S., Jun 2019, In : PLoS computational biology. 15, 6, e1007150.

Research output: Contribution to journalArticle

Open Access

Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments

Kouřil, D., Čmolík, L., Kozlíková, B., Wu, H. Y., Johnson, G., Goodsell, D. S., Olson, A., Gröller, M. E. & Viola, I., Jan 2019, In : IEEE Transactions on Visualization and Computer Graphics. 25, 1, p. 977-986 10 p., 8440077.

Research output: Contribution to journalArticle

6 Scopus citations

Late-onset retinal degeneration pathology due to mutations in CTRP5 is mediated through HTRA1

Chekuri, A., Zientara-Rytter, K., Soto-Hermida, A., Borooah, S., Voronchikhina, M., Biswas, P., Kumar, V., Goodsell, D., Hayward, C., Shaw, P., Stanton, C., Garland, D., Subramani, S. & Ayyagari, R., Dec 1 2019, In : Aging cell. 18, 6, e13011.

Research output: Contribution to journalArticle

Open Access

Novel intersubunit interaction critical for hiv-1 core assembly defines a potentially targetable inhibitor binding pocket

Craveur, P., Gres, A. T., Kirby, K. A., Liu, D., Hammond, J. A., Deng, Y., Forli, S., Goodsell, D. S., Williamson, J. R., Sarafianos, S. G. & Olson, A. J., Mar 1 2019, In : mBio. 10, 2, e02858-18.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Parallel Generation and Visualization of Bacterial Genome Structures

Klein, T., Mindek, P., Autin, L., Goodsell, D. S., Olson, A. J., Gröller, E. M. & Viola, I., Oct 1 2019, In : Computer Graphics Forum. 38, 7, p. 57-68 12 p.

Research output: Contribution to journalArticle

Protein Data Bank: The single global archive for 3D macromolecular structure data

WwPDB consortium, Jan 8 2019, In : Nucleic acids research. 47, D1, p. D520-D528

Research output: Contribution to journalArticle

Open Access
47 Scopus citations

RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., Christie, C., Dalenberg, K., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., Kalro, T., Liang, Y., Lowe, R. & 20 others, Namkoong, H., Peisach, E., Periskova, I., Prlić, A., Randle, C., Rose, A., Rose, P., Sala, R., Sekharan, M., Shao, C., Tan, L., Tao, Y. P., Valasatava, Y., Voigt, M., Westbrook, J., Woo, J., Yang, H., Young, J., Zhuravleva, M. & Zardecki, C., Jan 8 2019, In : Nucleic acids research. 47, D1, p. D464-D474

Research output: Contribution to journalArticle

61 Scopus citations
2018

CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments

Gardner, A., Autin, L., Barbaro, B., Olson, A. J. & Goodsell, D. S., Nov 1 2018, In : IEEE Computer Graphics and Applications. 38, 6, p. 51-64 14 p., 8617734.

Research output: Contribution to journalArticle

4 Scopus citations

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Goodsell, D. S., Franzen, M. A. & Herman, T., Oct 19 2018, In : Journal of molecular biology. 430, 21, p. 3954-3968 15 p.

Research output: Contribution to journalReview article

8 Scopus citations

Instant Construction and Visualization of Crowded Biological Environments

Klein, T., Autin, L., Kozlíková, B., Goodsell, D. S., Olson, A., Gröller, M. E. & Viola, I., Jan 2018, In : IEEE Transactions on Visualization and Computer Graphics. 24, 1, p. 862-872 11 p., 8019859.

Research output: Contribution to journalArticle

15 Scopus citations

Lattice Models of Bacterial Nucleoids

Goodsell, D. S., Autin, L. & Olson, A. J., May 31 2018, In : Journal of Physical Chemistry B. 122, 21, p. 5441-5447 7 p.

Research output: Contribution to journalArticle

8 Scopus citations

Molecular Illustration in Research and Education: Past, Present, and Future

Goodsell, D. S. & Jenkinson, J., Oct 19 2018, In : Journal of molecular biology. 430, 21, p. 3969-3981 13 p.

Research output: Contribution to journalReview article

5 Scopus citations
2017

A visual review of the human pathogen Streptococcus pneumoniae

Engholm, D. H., Kilian, M., Goodsell, D. S., Andersen, E. S. & Kjærgaard, R. S., Nov 1 2017, In : FEMS Microbiology Reviews. 41, 6, p. 854-879 26 p.

Research output: Contribution to journalReview article

7 Scopus citations

The RCSB protein data bank: Integrative view of protein, gene and 3D structural information

Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Green, R. K., Goodsell, D. S., Hudson, B., Kalro, T., Lowe, R., Peisach, E., Randle, C., Rose, A. S., Shao, C., Tao, Y. P. & 9 others, Valasatava, Y., Voigt, M., Westbrook, J. D., Woo, J., Yang, H., Young, J. Y., Zardecki, C., Berman, H. M. & Burley, S. K., Jan 1 2017, In : Nucleic acids research. 45, D1, p. D271-D281

Research output: Contribution to journalArticle

284 Scopus citations

Visualizing the Bacterium Streptococcus pneumoniae

Enghølm, D. H., Goodsell, D., Kilian, M., Andersen, E. S., Pedersen, B. P. & Kjærgaard, R. S., Aug 22 2017, The Aesthetics of Scientific Data Representation: More than Pretty Pictures. Taylor and Francis, p. 1-15 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2016

Computational protein-ligand docking and virtual drug screening with the AutoDock suite

Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S. & Olson, A. J., May 1 2016, In : Nature Protocols. 11, 5, p. 905-919 15 p.

Research output: Contribution to journalArticle

238 Scopus citations

Covalent docking using autodock: Two-point attractor and flexible side chain methods

Bianco, G., Forli, S., Goodsell, D. S. & Olson, A. J., Jan 1 2016, In : Protein Science. 25, 1, p. 295-301 7 p.

Research output: Contribution to journalArticle

50 Scopus citations

Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives

Belew, R. K., Forli, S., Goodsell, D. S., O'Donnell, T. J. & Olson, A. J., Aug 22 2016, In : Journal of Chemical Information and Modeling. 56, 8, p. 1597-1607 11 p.

Research output: Contribution to journalArticle

1 Scopus citations
16 Scopus citations

Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models

Le Muzic, M., Mindek, P., Sorger, J., Autin, L., Goodsell, D. S. & Viola, I., Jun 1 2016, In : Computer Graphics Forum. 35, 3, p. 161-170 10 p.

Research output: Contribution to journalArticle

8 Scopus citations

Winner of the 2016 Wellcome Image Awards

Goodsell, D., Apr 2 2016, In : Journal of Visual Communication in Medicine. 39, 1-2, 1 p.

Research output: Contribution to journalArticle

2015

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J. & Sanner, M. F., Jan 1 2015, In : PLoS computational biology. 11, 12, e1004586.

Research output: Contribution to journalArticle

40 Scopus citations

Illustrations of the HIV life cycle

Goodsell, D. S., Feb 26 2015, In : Current topics in microbiology and immunology. 389, p. 243-252 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Preface

Torbett, B. E., Goodsell, D. S. & Richman, D. D., Jan 1 2015, In : Current topics in microbiology and immunology. 389, p. v-vii

Research output: Contribution to journalEditorial

The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology

Goodsell, D. S., Dutta, S., Zardecki, C., Voigt, M., Berman, H. M. & Burley, S. K., May 5 2015, In : PLoS biology. 13, 5, e1002140.

Research output: Contribution to journalArticle

29 Scopus citations

The RCSB Protein Data Bank: Views of structural biology for basic and applied research and education

Rose, P. W., Prlić, 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., Jan 28 2015, In : Nucleic acids research. 43, D1, p. D345-D356

Research output: Contribution to journalArticle

298 Scopus citations
2014

3D molecular models of whole HIV-1 virions generated with cellPACK

Johnson, G. T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M. F. & Olson, A. J., Nov 1 2014, In : Faraday Discussions. 169, p. 23-44 22 p.

Research output: Contribution to journalArticle

20 Scopus citations

CellPACK: A virtual mesoscope to model and visualize structural systems biology

Johnson, G. T., Autin, L., Al-Alusi, M., Goodsell, D. S., Sanner, M. F. & Olson, A. J., Jan 1 2014, In : Nature Methods. 12, 1, p. 85-91 7 p.

Research output: Contribution to journalArticle

48 Scopus citations

Visualising microorganisms from molecules to cells

Goodsell, D. S. & Haas, D., Jul 2014, In : FEMS Microbiology Letters. 356, 1, p. 1-7 7 p.

Research output: Contribution to journalArticle

2013

Protein structure in context: The molecular landscape of angiogenesis

Span, E. A., Goodsell, D. S., Ramchandran, R., Franzen, M. A., Herman, T. & Sem, D. S., Jul 1 2013, In : Biochemistry and Molecular Biology Education. 41, 4, p. 213-223 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

Revealing structural views of biology

Goodsell, D. S., Burley, S. K. & Berman, H. M., Nov 1 2013, In : Biopolymers. 99, 11, p. 817-824 8 p.

Research output: Contribution to journalReview article

4 Scopus citations

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

Batiza, A. F., Gruhl, M., Zhang, B., Harrington, T., Roberts, M., La, D. F., Haasch, M. A., Knopp, J., Vogt, G., Goodsell, D., Hagedorn, E., Marcey, D., Hoelzer, M. & Nelson, D., Jun 12 2013, In : CBE Life Sciences Education. 12, 2, p. 287-305 19 p.

Research output: Contribution to journalArticle

2 Scopus citations

The RCSB Protein Data Bank: New resources for research and education

Rose, P. W., Bi, C., Bluhm, W. F., Christie, C. H., Dimitropoulos, D., Dutta, S., Green, R. K., Goodsell, D. S., Prlić, A., Quesada, M., Quinn, G. B., Ramos, A. G., Westbrook, J. D., Young, J., Zardecki, C., Berman, H. M. & Bourne, P. E., Jan 1 2013, In : Nucleic acids research. 41, D1, p. D475-D482

Research output: Contribution to journalArticle

302 Scopus citations

The twists and turns of DNA

Goodsell, D. S., 2013, In : Biologist. 60, 6, p. 18-22 5 p.

Research output: Contribution to journalComment/debate

2012

Illustrating the machinery of life: Viruses

Goodsell, D. S., Sep 1 2012, In : Biochemistry and Molecular Biology Education. 40, 5, p. 291-296 6 p.

Research output: Contribution to journalArticle

8 Scopus citations

Protein flexibility in virtual screening: The BACE-1 case study

Cosconati, S., Marinelli, L., Di Leva, F. S., La Pietra, V., De Simone, A., Mancini, F., Andrisano, V., Novellino, E., Goodsell, D. S. & Olson, A. J., Oct 22 2012, In : Journal of Chemical Information and Modeling. 52, 10, p. 2697-2704 8 p.

Research output: Contribution to journalArticle

38 Scopus citations
2011

Atomic evidence:The foundations of structural molecular biology

Goodsell, D., Dec 1 2011, In : Science Progress. 94, 4, p. 414-430 17 p.

Research output: Contribution to journalArticle

1 Scopus citations

ePMV embeds molecular modeling into professional animation software environments

Johnson, G. T., Autin, L., Goodsell, D. S., Sanner, M. F. & Olson, A. J., Mar 9 2011, In : Structure. 19, 3, p. 293-303 11 p.

Research output: Contribution to journalArticle

51 Scopus citations

Miniseries: Illustrating the machinery of life: Eukaryotic cell panorama

Goodsell, D. S., Mar 1 2011, In : Biochemistry and Molecular Biology Education. 39, 2, p. 91-101 11 p.

Research output: Contribution to journalArticle

19 Scopus citations

Redox-based probes for protein tyrosine phosphatases

Leonard, S. E., Garcia, F. J., Goodsell, D. S. & Carroll, K. S., May 2 2011, In : Angewandte Chemie - International Edition. 50, 19, p. 4423-4427 5 p.

Research output: Contribution to journalArticle

42 Scopus citations

The evolution of the RCSB Protein Data Bank website

Bourne, P. E., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Feng, Z., Goodsell, D. S., Prlić, A., Quinn, G. B., Rose, P. W., Westbrook, J., Yukich, B., Young, J., Zardecki, C. & Berman, H. M., Sep 1 2011, In : Wiley Interdisciplinary Reviews: Computational Molecular Science. 1, 5, p. 782-789 8 p.

Research output: Contribution to journalArticle

5 Scopus citations

The RCSB Protein Data Bank: Redesigned web site and web services

Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., Prlić, A., Quesada, M., Quinn, G. B., Westbrook, J. D., Young, J., Yukich, B., Zardecki, C., Berman, H. M. & Bourne, P. E., Jan 1 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D392-D401

Research output: Contribution to journalArticle

388 Scopus citations
2010

Artophagy: The art of autophagy - The Cvt pathway

Goodsell, D. S. & Klionsky, D. J., Jan 1 2010, In : Autophagy. 6, 1, p. 3-6 4 p.

Research output: Contribution to journalReview article

10 Scopus citations

Miniseries: Illustrating the machinery of life mitochondrion*

Goodsell, D. S., May 1 2010, In : Biochemistry and Molecular Biology Education. 38, 3, p. 134-140 7 p.

Research output: Contribution to journalArticle

4 Scopus citations

Promoting a structural view of biology for varied audiences: An overview of RCSB PDB resources and experiences

Dutta, S., Zardecki, C., Goodsell, D. S. & Berman, H. M., Oct 8 2010, In : Journal of Applied Crystallography. 43, 5 PART 2, p. 1224-1229 6 p.

Research output: Contribution to journalArticle

16 Scopus citations

Virtual screening with AutoDock: Theory and practice

Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D. S. & Olson, A. J., Jun 1 2010, In : Expert Opinion on Drug Discovery. 5, 6, p. 597-607 11 p.

Research output: Contribution to journalReview article

249 Scopus citations