Search Results - "Goddard, Thomas D"

UCSF ChimeraX: Tools for structure building and analysis by Meng, Elaine C., Goddard, Thomas D., Pettersen, Eric F., Couch, Greg S., Pearson, Zach J., Morris, John H., Ferrin, Thomas E.

“…Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at…”
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UCSF ChimeraX: Structure visualization for researchers, educators, and developers by Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Couch, Gregory S., Croll, Tristan I., Morris, John H., Ferrin, Thomas E.

“…UCSF ChimeraX is the next‐generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following…”
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UCSF ChimeraX: Meeting modern challenges in visualization and analysis by Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Pettersen, Eric F., Couch, Gregory S., Morris, John H., Ferrin, Thomas E.

“…UCSF ChimeraX is next‐generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It…”
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Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions by Pintilie, Grigore D., Zhang, Junjie, Goddard, Thomas D., Chiu, Wah, Gossard, David C.

“…Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation…”
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Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes by Fritz-Laylin, Lillian K, Riel-Mehan, Megan, Chen, Bi-Chang, Lord, Samuel J, Goddard, Thomas D, Ferrin, Thomas E, Nicholson-Dykstra, Susan M, Higgs, Henry, Johnson, Graham T, Betzig, Eric, Mullins, R Dyche

“…Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the…”
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UCSF Chimera-A visualization system for exploratory research and analysis by Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Couch, Gregory S., Greenblatt, Daniel M., Meng, Elaine C., Ferrin, Thomas E.

“…The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides…”
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Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins by Hertig, Samuel, Goddard, Thomas D., Johnson, Graham T., Ferrin, Thomas E.

“…Homology modeling predicts protein structures using known structures of related proteins as templates. We developed MULTIDOMAIN ASSEMBLER (MDA) to address the…”
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Visualization software for molecular assemblies by Goddard, Thomas D, Ferrin, Thomas E

“…Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments, and other molecular assemblies is advancing on many fronts. New…”
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UCSF Chimera, MODELLER, and IMP: An integrated modeling system by Yang, Zheng, Lasker, Keren, Schneidman-Duhovny, Dina, Webb, Ben, Huang, Conrad C., Pettersen, Eric F., Goddard, Thomas D., Meng, Elaine C., Sali, Andrej, Ferrin, Thomas E.

“…Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several…”
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Visualizing density maps with UCSF Chimera by Goddard, Thomas D., Huang, Conrad C., Ferrin, Thomas E.

“…We describe methods for interactive visualization and analysis of density maps available in the UCSF Chimera molecular modeling package. The methods enable…”
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Molecular Visualization on the Holodeck by Goddard, Thomas D., Brilliant, Alan A., Skillman, Thomas L., Vergenz, Steven, Tyrwhitt-Drake, James, Meng, Elaine C., Ferrin, Thomas E.

“…Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies…”
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Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures by Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick R., Haas, Juergen, Hanke, Christian A., Hoch, Jeffrey C., Hummer, Gerhard, Kurisu, Genji, Lawson, Catherine L., Leitner, Alexander, Markley, John L., Meiler, Jens, Montelione, Gaetano T., Phillips, George N., Prisner, Thomas, Rappsilber, Juri, Schriemer, David C., Schwede, Torsten, Seidel, Claus A.M., Strutzenberg, Timothy S., Svergun, Dmitri I., Tajkhorshid, Emad, Trewhella, Jill, Vallat, Brinda, Velankar, Sameer, Vuister, Geerten W., Webb, Benjamin, Westbrook, John D., White, Kate L., Sali, Andrej

“…Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining…”
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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods by Vallat, Brinda, Webb, Benjamin M., Westbrook, John D., Goddard, Thomas D., Hanke, Christian A., Graziadei, Andrea, Peisach, Ezra, Zalevsky, Arthur, Sagendorf, Jared, Tangmunarunkit, Hongsuda, Voinea, Serban, Sekharan, Monica, Yu, Jian, Bonvin, Alexander A.M.J.J., DiMaio, Frank, Hummer, Gerhard, Meiler, Jens, Tajkhorshid, Emad, Ferrin, Thomas E., Lawson, Catherine L., Leitner, Alexander, Rappsilber, Juri, Seidel, Claus A.M., Jeffries, Cy M., Burley, Stephen K., Hoch, Jeffrey C., Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, Velankar, Sameer, Schwede, Torsten, Trewhella, Jill, Kesselman, Carl, Berman, Helen M., Sali, Andrej

“…[Display omitted] •Data standard for macromolecular structures from integrative and hybrid modeling (IHM).•Infrastructure for deposition, archiving, and public…”
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Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies by Goddard, Thomas D., Huang, Conrad C., Ferrin, Thomas E.

“…Many structures of large molecular assemblies such as virus capsids and ribosomes have been experimentally determined to atomic resolution. We consider four…”
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Long-range interphase chromosome organization in Drosophila: a study using color barcoded fluorescence in situ hybridization and structural clustering analysis by Lowenstein, Michael G, Goddard, Thomas D, Sedat, John W

“…We have developed a color barcode labeling strategy for use with fluorescence in situ hybridization that enables the discrimination of multiple, identically…”
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Long-Range Interphase Chromosome Organization in Drosophila: A Study Using Color Barcoded Fluorescence In Situ Hybridization and Structural Clustering AnalysisD by Lowenstein, Michael G., Goddard, Thomas D., Sedat, John W.

“…We have developed a color barcode labeling strategy for use with fluorescence in situ hybridization that enables the discrimination of multiple, identically…”
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