Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks

Frontiers in Bioengineering and Biotechnology
Chun-Ting YehFabio Parmeggiani

Abstract

Molecular models have enabled understanding of biological structures and functions and allowed design of novel macro-molecules. Graphical user interfaces (GUIs) in molecular modeling are generally focused on atomic representations, but, especially for proteins, do not usually address designs of complex and large architectures, from nanometers to microns. Therefore, we have developed Elfin UI as a Blender add-on for the interactive design of large protein architectures with custom shapes. Elfin UI relies on compatible building blocks to design single- and multiple-chain protein structures. The software can be used: (1) as an interactive environment to explore building blocks combinations; and (2) as a computer aided design (CAD) tool to define target shapes that guide automated design. Elfin UI allows users to rapidly build new protein shapes, without the need to focus on amino acid sequence, and aims to make design of proteins and protein-based materials intuitive and accessible to researchers and members of the general public with limited expertise in protein engineering.

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Jun 18, 2009·Nucleic Acids Research·Shawn M DouglasWilliam M Shih
Aug 6, 2010·Nature·Seth CooperFoldit Players
Sep 21, 2010·Journal of Molecular Biology·Michaela A KramerMarkus G Grütter
Mar 15, 2011·Structure·Graham T JohnsonArthur J Olson
May 2, 2012·BMC Bioinformatics·Raluca Mihaela AndreiMonica Zoppè
Apr 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christopher J LanciJeffery G Saven
Jun 2, 2012·Science·Yen-Ting LaiTodd O Yeates
Nov 9, 2012·Nature·Nobuyasu KogaDavid Baker
Jun 15, 2013·Journal of the American Chemical Society·Anna GrochmalSalvador Tomas
Jul 23, 2013·PloS One·Jared Adolf-Bryfogle, Roland L Dunbrack
Jul 7, 2014·Nature Methods·Alan ShawAna I Teixeira
Sep 24, 2014·Nature Reviews. Molecular Cell Biology·Graham T Johnson, Samuel Hertig
Jul 24, 2015·Nature·Erik BensonBjörn Högberg
Sep 1, 2015·Bioinformatics·Christian D Schenkelberg, Christopher Bystroff
Apr 18, 2016·Current Opinion in Structural Biology·Pablo GainzaBruce R Donald
May 28, 2016·Science·Rémi VenezianoMark Bathe
Mar 8, 2017·Current Opinion in Structural Biology·Fabio Parmeggiani, Po-Ssu Huang
Mar 25, 2017·Nature Chemistry·Jorge A FallasDavid Baker
Sep 13, 2017·Scientific Reports·Yufan WuAndreas Plückthun
Oct 17, 2017·Nature Biotechnology·Ajasja LjubetičRoman Jerala
Dec 28, 2017·Journal of Computational Chemistry·Nivedita Rajendiran, Jacob D Durrant
Nov 28, 2018·Bioinformatics·Jacob D Durrant
Apr 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·T J BrunetteDavid Baker
Jun 3, 2020·Nature Methods·Julia Koehler LemanRichard Bonneau

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Citations

Mar 16, 2021·Current Opinion in Structural Biology·Frances Gidley, Fabio Parmeggiani

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Methods Mentioned

BETA
protein folding

Software Mentioned

vHelix
BlendMol
Elfin Solver
Blender
Elfin UI
JSON
CanDo
PyMOL Molecular Graphics System
PyMOL
elfin

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