• 28988 Citations
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1985 …2020

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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
2 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
8 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
1 Scopus citations

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

1 Scopus citations

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
75 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

106 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

5 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

16 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

9 Scopus citations
2017

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

302 Scopus citations
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

268 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

56 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

48 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

12 Scopus citations

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

31 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

305 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

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

311 Scopus citations
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

39 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

52 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

20 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

392 Scopus citations
2010

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
2009

Computational docking of biomolecular complexes with autodock

Goodsell, D., Aug 13 2009, In : Cold Spring Harbor Protocols. 4, 5

Research output: Contribution to journalArticle

19 Scopus citations

Escherichia coli

Goodsell, D. S., Nov 1 2009, In : Biochemistry and Molecular Biology Education. 37, 6, p. 325-332 8 p.

Research output: Contribution to journalArticle

17 Scopus citations

Fact and fantasy in nanotech imagery

Goodsell, D., Jan 1 2009, In : Leonardo. 42, 1, p. 52-57 6 p.

Research output: Contribution to journalArticle

12 Scopus citations

Neuromuscular synapse

Goodsell, D. S., Jul 1 2009, In : Biochemistry and Molecular Biology Education. 37, 4, p. 204-210 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Morris, G. M., Ruth, H., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. J., Dec 1 2009, In : Journal of Computational Chemistry. 30, 16, p. 2785-2791 7 p.

Research output: Contribution to journalArticle

7561 Scopus citations
2008

Automated prediction of ligand-binding sites in proteins

Harris, R., Olson, A. J. & Goodsell, D. S., Mar 1 2008, In : Proteins: Structure, Function and Genetics. 70, 4, p. 1506-1517 12 p.

Research output: Contribution to journalArticle

70 Scopus citations

Empirical entropie contributions in computational docking: Evaluation in APS reductase complexes

Chang, M. W., Belew, R. K., Carroll, K. S., Olson, A. J. & Goodsell, D. S., Aug 1 2008, In : Journal of Computational Chemistry. 29, 11, p. 1753-1761 9 p.

Research output: Contribution to journalArticle

31 Scopus citations

Structure-based virtual screening and biological evaluation of Mycobacterium tuberculosis adenosine 5′-phosphosulfate reductase inhibitors

Cosconati, S., Hong, J. A., Novellino, E., Carroll, K. S., Goodsell, D. & Olson, A. J., Nov 13 2008, In : Journal of Medicinal Chemistry. 51, 21, p. 6627-6630 4 p.

Research output: Contribution to journalArticle

33 Scopus citations
2007

Software news and update a semiempirical free energy force field with charge-based desolvation

Huey, R., Morris, G. M., Olson, A. J. & Goodsell, D. S., Apr 30 2007, In : Journal of Computational Chemistry. 28, 6, p. 1145-1152 8 p.

Research output: Contribution to journalArticle

1432 Scopus citations
2006

Recognition highlights: Toll-like receptors

Goodsell, D. S., Sep 1 2006, In : Journal of Molecular Recognition. 19, 5, p. 387-388 2 p.

Research output: Contribution to journalArticle

Seeing the nanoscale

Goodsell, D. S., Aug 1 2006, In : Nano Today. 1, 3, p. 44-49 6 p.

Research output: Contribution to journalArticle

11 Scopus citations

The molecular perspective: Alcohol

Goodsell, D. S., Oct 1 2006, In : Oncologist. 11, 9, p. 1045-1046 2 p.

Research output: Contribution to journalArticle

6 Scopus citations