Literature DB >> 29885327

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

David S Goodsell1, Margaret A Franzen2, Tim Herman2.   

Abstract

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.
Copyright © 2018 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  cellular mesoscale; integrative structural biology; mesoscale modeling; molecular graphics; science education

Mesh：

Year:  2018        PMID： 29885327      PMCID： PMC6186495          DOI： 10.1016/j.jmb.2018.06.009

Source DB:  PubMed          Journal:  J Mol Biol        ISSN： 0022-2836            Impact factor:   5.469


  47 in total

1.  Inferential structure determination.

Authors:  Wolfgang Rieping; Michael Habeck; Michael Nilges
Journal:  Science       Date:  2005-07-08       Impact factor: 47.728

Review 2.  Inside a living cell.

Authors:  D S Goodsell
Journal:  Trends Biochem Sci       Date:  1991-06       Impact factor: 13.807

3.  Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models.

Authors:  M Le Muzic; P Mindek; J Sorger; L Autin; D Goodsell; I Viola
Journal:  Comput Graph Forum       Date:  2016-06       Impact factor: 2.078

Review 4.  Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?

Authors:  Martin Beck; Wolfgang Baumeister
Journal:  Trends Cell Biol       Date:  2016-09-23       Impact factor: 20.808

5.  Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome.

Authors:  Suckjoon Jun; Bela Mulder
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-02       Impact factor: 11.205

Review 6.  Discovery through the computational microscope.

Authors:  Eric H Lee; Jen Hsin; Marcos Sotomayor; Gemma Comellas; Klaus Schulten
Journal:  Structure       Date:  2009-10-14       Impact factor: 5.006

7.  Protein structure in context: the molecular landscape of angiogenesis.

Authors:  Elise A Span; David S Goodsell; Ramani Ramchandran; Margaret A Franzen; Tim Herman; Daniel S Sem
Journal:  Biochem Mol Biol Educ       Date:  2013 Jul-Aug       Impact factor: 1.160

8.  A subcellular map of the human proteome.

Authors:  Peter J Thul; Lovisa Åkesson; Mikaela Wiking; Diana Mahdessian; Aikaterini Geladaki; Hammou Ait Blal; Tove Alm; Anna Asplund; Lars Björk; Lisa M Breckels; Anna Bäckström; Frida Danielsson; Linn Fagerberg; Jenny Fall; Laurent Gatto; Christian Gnann; Sophia Hober; Martin Hjelmare; Fredric Johansson; Sunjae Lee; Cecilia Lindskog; Jan Mulder; Claire M Mulvey; Peter Nilsson; Per Oksvold; Johan Rockberg; Rutger Schutten; Jochen M Schwenk; Åsa Sivertsson; Evelina Sjöstedt; Marie Skogs; Charlotte Stadler; Devin P Sullivan; Hanna Tegel; Casper Winsnes; Cheng Zhang; Martin Zwahlen; Adil Mardinoglu; Fredrik Pontén; Kalle von Feilitzen; Kathryn S Lilley; Mathias Uhlén; Emma Lundberg
Journal:  Science       Date:  2017-05-11       Impact factor: 47.728

9.  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.

Authors:  Ann Finney Batiza; Mary Gruhl; Bo Zhang; Tom Harrington; Marisa Roberts; Donna LaFlamme; Mary Anne Haasch; Jonathan Knopp; Gina Vogt; David Goodsell; Eric Hagedorn; David Marcey; Mark Hoelzer; Dave Nelson
Journal:  CBE Life Sci Educ       Date:  2013-06-01       Impact factor: 3.325

10.  LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.

Authors:  Jacob D Durrant; Rommie E Amaro
Journal:  PLoS Comput Biol       Date:  2014-07-17       Impact factor: 4.475
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  8 in total

Review 1.  Challenges in protein docking.

Authors:  Ilya A Vakser
Journal:  Curr Opin Struct Biol       Date:  2020-08-21       Impact factor: 6.809

2.  Building Structural Models of a Whole Mycoplasma Cell.

Authors:  Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal:  J Mol Biol       Date:  2021-11-10       Impact factor: 5.469

3.  Bayesian metamodeling of complex biological systems across varying representations.

Authors:  Barak Raveh; Liping Sun; Kate L White; Tanmoy Sanyal; Jeremy Tempkin; Dongqing Zheng; Kala Bharath; Jitin Singla; Chenxi Wang; Jihui Zhao; Angdi Li; Nicholas A Graham; Carl Kesselman; Raymond C Stevens; Andrej Sali
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-31       Impact factor: 11.205

Review 4.  Art and Science of the Cellular Mesoscale.

Authors:  David S Goodsell; Arthur J Olson; Stefano Forli
Journal:  Trends Biochem Sci       Date:  2020-03-21       Impact factor: 13.807

5.  PDB-101: Educational resources supporting molecular explorations through biology and medicine.

Authors:  Christine Zardecki; Shuchismita Dutta; David S Goodsell; Robert Lowe; Maria Voigt; Stephen K Burley
Journal:  Protein Sci       Date:  2021-10-18       Impact factor: 6.725

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

7.  Integrative illustration of a JCVI-syn3A minimal cell.

Authors:  David S Goodsell
Journal:  J Integr Bioinform       Date:  2022-06-27

8.  Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus.

Authors:  Jingwei Ma; Myan Do; Mark A Le Gros; Charles S Peskin; Carolyn A Larabell; Yoichiro Mori; Samuel A Isaacson
Journal:  PLoS Comput Biol       Date:  2020-11-16       Impact factor: 4.779
  8 in total

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