Literature DB >> 32413324

Art and Science of the Cellular Mesoscale.

David S Goodsell1, Arthur J Olson2, Stefano Forli2.   

Abstract

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  cell function; cell structure; drug design; drug discovery; integrative structural biology; mesoscale modeling; molecular function; molecular structure

Year:  2020        PMID: 32413324      PMCID: PMC7230070          DOI: 10.1016/j.tibs.2020.02.010

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  68 in total

Review 1.  Composition, architecture and dynamics of the photosynthetic apparatus in higher plants.

Authors:  Reinat Nevo; Dana Charuvi; Onie Tsabari; Ziv Reich
Journal:  Plant J       Date:  2012-04       Impact factor: 6.417

2.  Molecular anatomy of a trafficking organelle.

Authors:  Shigeo Takamori; Matthew Holt; Katinka Stenius; Edward A Lemke; Mads Grønborg; Dietmar Riedel; Henning Urlaub; Stephan Schenck; Britta Brügger; Philippe Ringler; Shirley A Müller; Burkhard Rammner; Frauke Gräter; Jochen S Hub; Bert L De Groot; Gottfried Mieskes; Yoshinori Moriyama; Jürgen Klingauf; Helmut Grubmüller; John Heuser; Felix Wieland; Reinhard Jahn
Journal:  Cell       Date:  2006-11-17       Impact factor: 41.582

3.  Modeling Viral Capsid Assembly.

Authors:  Michael F Hagan
Journal:  Adv Chem Phys       Date:  2014       Impact factor: 1.000

4.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

5.  UCSF ChimeraX: Meeting modern challenges in visualization and analysis.

Authors:  Thomas D Goddard; Conrad C Huang; Elaine C Meng; Eric F Pettersen; Gregory S Couch; John H Morris; Thomas E Ferrin
Journal:  Protein Sci       Date:  2017-09-06       Impact factor: 6.725

6.  cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets.

Authors:  Mathieu Le Muzic; Ludovic Autin; Julius Parulek; Ivan Viola
Journal:  Eurographics Workshop Vis Comput Biomed       Date:  2015

Review 7.  Macromolecular Crowding In Vitro, In Vivo, and In Between.

Authors:  Germán Rivas; Allen P Minton
Journal:  Trends Biochem Sci       Date:  2016-09-23       Impact factor: 13.807

8.  Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

Authors:  Sean R McGuffee; Adrian H Elcock
Journal:  PLoS Comput Biol       Date:  2010-03-05       Impact factor: 4.475

9.  Lattice Models of Bacterial Nucleoids.

Authors:  David S Goodsell; Ludovic Autin; Arthur J Olson
Journal:  J Phys Chem B       Date:  2018-01-25       Impact factor: 2.991

10.  Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.

Authors:  Daniel Russel; Keren Lasker; Ben Webb; Javier Velázquez-Muriel; Elina Tjioe; Dina Schneidman-Duhovny; Bret Peterson; Andrej Sali
Journal:  PLoS Biol       Date:  2012-01-17       Impact factor: 8.029

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  6 in total

1.  Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes.

Authors:  Terry J McGenity; Amare Gessesse; John E Hallsworth; Esther Garcia Cela; Carol Verheecke-Vaessen; Fengping Wang; Max Chavarría; Max M Haggblom; Søren Molin; Antoine Danchin; Eddy J Smid; Cédric Lood; Charles S Cockell; Corinne Whitby; Shuang-Jiang Liu; Nancy P Keller; Lisa Y Stein; Seth R Bordenstein; Rup Lal; Olga C Nunes; Lone Gram; Brajesh K Singh; Nicole S Webster; Cindy Morris; Sharon Sivinski; Saskia Bindschedler; Pilar Junier; André Antunes; Bonnie K Baxter; Paola Scavone; Kenneth Timmis
Journal:  Microb Biotechnol       Date:  2020-05-14       Impact factor: 5.813

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.  Visualizing Presynaptic Active Zones and Synaptic Vesicles.

Authors:  Manfred Heckmann; Martin Pauli
Journal:  Front Synaptic Neurosci       Date:  2022-05-18

4.  Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.

Authors:  Ngan Nguyen; Ondrej Strnad; Tobias Klein; Deng Luo; Ruwayda Alharbi; Peter Wonka; Martina Maritan; Peter Mindek; Ludovic Autin; David S Goodsell; Ivan Viola
Journal:  IEEE Trans Vis Comput Graph       Date:  2021-01-28       Impact factor: 4.579

5.  CellPAINT: Turnkey Illustration of Molecular Cell Biology.

Authors:  Adam Gardner; Ludovic Autin; Daniel Fuentes; Martina Maritan; Benjamin A Barad; Michaela Medina; Arthur J Olson; Danielle A Grotjahn; David S Goodsell
Journal:  Front Bioinform       Date:  2021-03-29

6.  Considering best practices in color palettes for molecular visualizations.

Authors:  Laura Garrison; Stefan Bruckner
Journal:  J Integr Bioinform       Date:  2022-06-22
  6 in total

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