Literature DB >> 31519398

Illustrate: Software for Biomolecular Illustration.

David S Goodsell1, Ludovic Autin2, Arthur J Olson2.   

Abstract

The small program Illustrate generates non-photorealistic images of biological molecules for use in dissemination, outreach, and education. The method has been used as part of the "Molecule of the Month," an ongoing educational column at the RCSB Protein Data Bank (http://rcsb.org). Insights from 20 years of application of the program are presented, and the program has been released both as open-source Fortran at GitHub and through an interactive web-based interface.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  ambient occlusion; biomolecular visualization; computer graphics; non-photorealistic rendering; protein structure; science education

Mesh：

Year:  2019        PMID： 31519398      PMCID： PMC6834899          DOI： 10.1016/j.str.2019.08.011

Source DB:  PubMed          Journal:  Structure        ISSN： 0969-2126            Impact factor:   5.006


  9 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Molecular illustration in black and white.

Authors:  D S Goodsell; A J Olson
Journal:  J Mol Graph       Date:  1992-12

3.  Ambient occlusion and edge cueing to enhance real time molecular visualization.

Authors:  Marco Tarini; Paolo Cignoni; Claudio Montani
Journal:  IEEE Trans Vis Comput Graph       Date:  2006 Sep-Oct       Impact factor: 4.579

4.  Enhancement and simplification of macromolecular images.

Authors:  K Namba; D L Caspar; G Stubbs
Journal:  Biophys J       Date:  1988-04       Impact factor: 4.033

Review 5.  Perspectives on Structural Molecular Biology Visualization: From Past to Present.

Authors:  Arthur J Olson
Journal:  J Mol Biol       Date:  2018-07-23       Impact factor: 5.469

6.  CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments.

Authors:  Adam Gardner; Ludovic Autin; Brett Barbaro; Arthur J Olson; David S Goodsell
Journal:  IEEE Comput Graph Appl       Date:  2018 Nov-Dec       Impact factor: 2.088

7.  The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology.

Authors:  David S Goodsell; Shuchismita Dutta; Christine Zardecki; Maria Voigt; Helen M Berman; Stephen K Burley
Journal:  PLoS Biol       Date:  2015-05-05       Impact factor: 8.029

Review 8.  Visualization of macromolecular structures.

Authors:  Seán I O'Donoghue; David S Goodsell; Achilleas S Frangakis; Fabrice Jossinet; Roman A Laskowski; Michael Nilges; Helen R Saibil; Andrea Schafferhans; Rebecca C Wade; Eric Westhof; Arthur J Olson
Journal:  Nat Methods       Date:  2010-03-01       Impact factor: 28.547

9.  ProteinShader: illustrative rendering of macromolecules.

Authors:  Joseph R Weber
Journal:  BMC Struct Biol       Date:  2009-03-30
  9 in total
  31 in total

1.  Molecular storytelling for online structural biology outreach and education.

Authors:  David S Goodsell; Shuchismita Dutta; Maria Voigt; Christine Zardecki
Journal:  Struct Dyn       Date:  2021-03-05       Impact factor: 2.920

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Authors:  Harriet V Mears; Trevor R Sweeney
Journal:  J Biol Chem       Date:  2020-10-19       Impact factor: 5.157

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Authors:  Dillon T Flood; Xuejing Zhang; Xiang Fu; Zhenxiang Zhao; Shota Asai; Brittany B Sanchez; Emily J Sturgell; Julien C Vantourout; Paul Richardson; Mark E Flanagan; David W Piotrowski; Dominik K Kölmel; Jinqiao Wan; Mei-Hsuan Tsai; Jason S Chen; Phil S Baran; Philip E Dawson
Journal:  Angew Chem Int Ed Engl       Date:  2020-03-11       Impact factor: 15.336

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Authors:  Lucia Strader; Dolf Weijers; Doris Wagner
Journal:  Curr Opin Plant Biol       Date:  2021-11-29       Impact factor: 7.834

5.  Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.

Authors:  Rocco Meli; Garrett M Morris; Philip C Biggin
Journal:  Front Bioinform       Date:  2022-06-17

Review 6.  Targeted protein degradation as a powerful research tool in basic biology and drug target discovery.

Authors:  Tao Wu; Hojong Yoon; Yuan Xiong; Sarah E Dixon-Clarke; Radosław P Nowak; Eric S Fischer
Journal:  Nat Struct Mol Biol       Date:  2020-06-15       Impact factor: 15.369

7.  Physical tuning of galectin-3 signaling.

Authors:  Shaheen A Farhadi; Renjie Liu; Matthew W Becker; Edward A Phelps; Gregory A Hudalla
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-11       Impact factor: 11.205

8.  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

9.  Expression of selenoproteins via genetic code expansion in mammalian cells.

Authors:  Jennifer C Peeler; Eranthie Weerapana
Journal:  Methods Enzymol       Date:  2021-11-24       Impact factor: 1.682

10.  Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C.

Authors:  Austin M Cool; Steffen Lindert
Journal:  J Phys Chem B       Date:  2021-07-02       Impact factor: 3.466
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