Search Results - "Meng, Elaine C"

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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DOCK 6: combining techniques to model RNA-small molecule complexes by Lang, P Therese, Brozell, Scott R, Mukherjee, Sudipto, Pettersen, Eric F, Meng, Elaine C, Thomas, Veena, Rizzo, Robert C, Case, David A, James, Thomas L, Kuntz, Irwin D

“…With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design,…”
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Tools for integrated sequence-structure analysis with UCSF Chimera by Meng, Elaine C, Pettersen, Eric F, Couch, Gregory S, Huang, Conrad C, Ferrin, Thomas E

“…Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While…”
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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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Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data [version 2; peer review: 1 approved, 2 approved with reservations] by Diaz-Mejia, J. Javier, Meng, Elaine C, Pico, Alexander R, MacParland, Sonya A, Ketela, Troy, Pugh, Trevor J, Bader, Gary D, Morris, John H

“…Background: Identification of cell type subpopulations from complex cell mixtures using single-cell RNA-sequencing (scRNA-seq) data includes automated steps…”
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Apolipoprotein (Apo) E4 Enhances Amyloid β Peptide Production in Cultured Neuronal Cells: Apoe Structure as a Potential Therapeutic Target by Shiming Ye, Huang, Yadong, Karin Müllendorff, Liming Dong, Gretchen Giedt, Meng, Elaine C., Cohen, Fred E., Kuntz, Irwin D., Weisgraber, Karl H., Mahley, Robert W.

“…Apolipoprotein (apo) E4 is a major risk factor for Alzheimer's disease, and many studies have suggested that apoE has isoformspecific effects on the deposition…”
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Evolutionary Trace of G Protein-coupled Receptors Reveals Clusters of Residues That Determine Global and Class-specific Functions by Madabushi, Srinivasan, Gross, Alecia K., Philippi, Anne, Meng, Elaine C., Wensel, Theodore G., Lichtarge, Olivier

“…G protein-coupled receptor (GPCR) activation mediated by ligand-induced structural reorganization of its helices is poorly understood. To determine the…”
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scNetViz: from single cells to networks using Cytoscape by Choudhary, Krishna, Meng, Elaine C, Diaz-Mejia, J Javier, Bader, Gary D, Pico, Alexander R, Morris, John H

“…Single-cell RNA-sequencing (scRNA-seq) has revolutionized molecular biology and medicine by enabling high-throughput studies of cellular heterogeneity in…”
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Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design:  The Structure−Function Linkage Database by Pegg, Scott C.-H, Brown, Shoshana D, Ojha, Sunil, Seffernick, Jennifer, Meng, Elaine C, Morris, John H, Chang, Patricia J, Huang, Conrad C, Ferrin, Thomas E, Babbitt, Patricia C

“…The study of mechanistically diverse enzyme superfamiliescollections of enzymes that perform different overall reactions but share both a common fold and a…”
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Evolution of function in the "two dinucleotide binding domains" flavoproteins by Ojha, Sunil, Meng, Elaine C, Babbitt, Patricia C

“…Structural and biochemical constraints force some segments of proteins to evolve more slowly than others, often allowing identification of conserved structural…”
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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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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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Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data [version 3; peer review: 2 approved, 1 approved with reservations] by Diaz-Mejia, J. Javier, Meng, Elaine C, Pico, Alexander R, MacParland, Sonya A, Ketela, Troy, Pugh, Trevor J, Bader, Gary D, Morris, John H

“…Background: Identification of cell type subpopulations from complex cell mixtures using single-cell RNA-sequencing (scRNA-seq) data includes automated steps…”
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Enhancing UCSF Chimera through web services by Huang, Conrad C, Meng, Elaine C, Morris, John H, Pettersen, Eric F, Ferrin, Thomas E

“…Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive…”
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The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information by Morris, John H, Soman, Karthik, Akbas, Rabia E, Zhou, Xiaoyuan, Smith, Brett, Meng, Elaine C, Huang, Conrad C, Cerono, Gabriel, Schenk, Gundolf, Rizk-Jackson, Angela, Harroud, Adil, Sanders, Lauren, Costes, Sylvain V, Bharat, Krish, Chakraborty, Arjun, Pico, Alexander R, Mardirossian, Taline, Keiser, Michael, Tang, Alice, Hardi, Josef, Shi, Yongmei, Musen, Mark, Israni, Sharat, Huang, Sui, Rose, Peter W, Nelson, Charlotte A, Baranzini, Sergio E

“…Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity…”
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The Structure-Function Linkage Database by Akiva, Eyal, Brown, Shoshana, Almonacid, Daniel E, Barber, 2nd, Alan E, Custer, Ashley F, Hicks, Michael A, Huang, Conrad C, Lauck, Florian, Mashiyama, Susan T, Meng, Elaine C, Mischel, David, Morris, John H, Ojha, Sunil, Schnoes, Alexandra M, Stryke, Doug, Yunes, Jeffrey M, Ferrin, Thomas E, Holliday, Gemma L, Babbitt, Patricia C

“…The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function…”
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Likelihood‐based interactive local docking into cryo‐EM maps in ChimeraX by Read, Randy J., Pettersen, Eric F., McCoy, Airlie J., Croll, Tristan I., Terwilliger, Thomas C., Poon, Billy K., Meng, Elaine C., Liebschner, Dorothee, Adams, Paul D.

“…The interpretation of cryo‐EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map…”
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ModBase, a database of annotated comparative protein structure models, and associated resources by Pieper, Ursula, Webb, Benjamin M, Barkan, David T, Schneidman-Duhovny, Dina, Schlessinger, Avner, Braberg, Hannes, Yang, Zheng, Meng, Elaine C, Pettersen, Eric F, Huang, Conrad C, Datta, Ruchira S, Sampathkumar, Parthasarathy, Madhusudhan, Mallur S, Sjölander, Kimmen, Ferrin, Thomas E, Burley, Stephen K, Sali, Andrej

“…ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated…”
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