Molecular Illustration in Research and Education: Past, Present, and Future

Goodsell, David S.; Jenkinson, Jodie

doi:10.1016/j.jmb.2018.04.043

Cited by 53 publications

(29 citation statements)

References 54 publications

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“…2.2 Synchronized selection among 3D structure, 2D interactions, defined sets and 1D sequences and annotations 2D or 1D representations often convey information that is difficult to spot or highlight in complex 3D representations (Goodsell and Jenkinson, 2018;Heinrich et al, 2014;Munzner, 2014). To this end, iCn3D visualizes macromolecular complexes in 3D, 2D and 1D, and synchronizes the selection among the various representations.…”

Section: Share Linkmentioning

confidence: 99%

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

et al. 2019

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Motivation Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. Results iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure–structure alignments obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1. Availability and implementation iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Share Linkmentioning

confidence: 99%

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

et al. 2019

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“…To generate illustrative and compelling images for publications is another widespread and very common need reviewed by Goodsell and Jenkinson [27]. David Goodsell has provided for many years the captivating images of the molecule of the month [28], which can now be reproduced by everyone with the Illustrate software [29].…”

Section: Emerging Needs For Molecular Visualizationmentioning

confidence: 99%

Visualizing protein structures — tools and trends

Martinez

Chavent

Baaden

2020

Biochemical Society Transactions

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Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few ‘Swiss Army knives’ geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

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“…Lying deep within the cytoplasm, the atomic forms and actions of molecules can be more precisely studied in abstract and without cinematic license as described in a number of specific guidelines for molecular visualization [46]. Lipid membranes, small proteins and DNA components can be rendered as particle clouds, ball-and-stick diagrams or functionally descriptive "cartoons" [64]. Adopting the visual grammar of proteins is logical for close inspection but the crowded cytoplasm obligates greater clarity, for example by the use of distinct colored molecular glyphs (Fig.…”

Section: Representative Grammarmentioning

confidence: 99%

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Goodstadt

Martí‐Renom

2019

Journal of Molecular Biology

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Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.

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Molecular Illustration in Research and Education: Past, Present, and Future

Cited by 53 publications

References 54 publications

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

Visualizing protein structures — tools and trends

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

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