Literature DB >> 32061125

Michelanglo: sculpting protein views on web pages without coding.

Matteo P Ferla1,2,3, Alistair T Pagnamenta1,2, David Damerell3, Jenny C Taylor1,2, Brian D Marsden3,4.   

Abstract

MOTIVATION: The sharing of macromolecular structural information online by scientists is predominantly performed via two-dimensional static images, since the embedding of interactive 3D structures in webpages is non-trivial. Whilst the technologies to do so exist, they are often only implementable with significant web coding experience.
RESULTS: Michelanglo is an accessible and open-source web-based application that supports the generation, customisation and sharing of interactive three-dimensional macromolecular visualisations for digital media without requiring programming skills. A PyMOL file, PDB file, PDB identifier code or protein/gene name can be provided to form the basis of visualisations using the NGL JavaScript library. Hyperlinks that control the view can be added to text within the page. Protein-coding variants can be highlighted to support interpretation of their potential functional consequences. The resulting visualisations and text can be customised and shared, as well as embedded within existing web sites by following instructions and using a self-contained download. Michelanglo allows researchers to move away from static images and instead engage, describe and explain their protein to a wider audience in a more interactive fashion. AVAILABILITY: Michelanglo is hosted at michelanglo.sgc.ox.ac.uk. The Python code is freely available at github.com/thesgc/MichelaNGLo, along with documentations about its implementation.
© The Author(s) 2020. Published by Oxford University Press.

Entities:  

Year:  2020        PMID: 32061125     DOI: 10.1093/bioinformatics/btaa104

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  9 in total

1.  Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy.

Authors:  Dana Marafi; Jawid M Fatih; Rauan Kaiyrzhanov; Matteo P Ferla; Charul Gijavanekar; Aljazi Al-Maraghi; Ning Liu; Emily Sites; Hessa S Alsaif; Mohammad Al-Owain; Mohamed Zakkariah; Ehab El-Anany; Ulviyya Guliyeva; Sughra Guliyeva; Colette Gaba; Ateeq Haseeb; Amal M Alhashem; Enam Danish; Vasiliki Karageorgou; Christian Beetz; Alaa A Subhi; Sureni V Mullegama; Erin Torti; Monisha Sebastin; Margo Sheck Breilyn; Susan Duberstein; Mohamed S Abdel-Hamid; Tadahiro Mitani; Haowei Du; Jill A Rosenfeld; Shalini N Jhangiani; Zeynep Coban Akdemir; Richard A Gibbs; Jenny C Taylor; Khalid A Fakhro; Jill V Hunter; Davut Pehlivan; Maha S Zaki; Joseph G Gleeson; Reza Maroofian; Henry Houlden; Jennifer E Posey; V Reid Sutton; Fowzan S Alkuraya; Sarah H Elsea; James R Lupski
Journal:  Brain       Date:  2022-04-29       Impact factor: 15.255

2.  Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms.

Authors:  Caroline F Wright; Nicholas M Quaife; Laura Ramos-Hernández; Petr Danecek; Matteo P Ferla; Kaitlin E Samocha; Joanna Kaplanis; Eugene J Gardner; Ruth Y Eberhardt; Katherine R Chao; Konrad J Karczewski; Joannella Morales; Giuseppe Gallone; Meena Balasubramanian; Siddharth Banka; Lianne Gompertz; Bronwyn Kerr; Amelia Kirby; Sally A Lynch; Jenny E V Morton; Hailey Pinz; Francis H Sansbury; Helen Stewart; Britton D Zuccarelli; Stuart A Cook; Jenny C Taylor; Jane Juusola; Kyle Retterer; Helen V Firth; Matthew E Hurles; Enrique Lara-Pezzi; Paul J R Barton; Nicola Whiffin
Journal:  Am J Hum Genet       Date:  2021-05-21       Impact factor: 11.025

3.  An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy.

Authors:  Alistair T Pagnamenta; Rauan Kaiyrzhanov; Yaqun Zou; Sahar I Da'as; Reza Maroofian; Sandra Donkervoort; Natalia Dominik; Marlen Lauffer; Matteo P Ferla; Andrea Orioli; Adam Giess; Arianna Tucci; Christian Beetz; Maryam Sedghi; Behnaz Ansari; Rita Barresi; Keivan Basiri; Andrea Cortese; Greg Elgar; Miguel A Fernandez-Garcia; Janice Yip; A Reghan Foley; Nicholas Gutowski; Heinz Jungbluth; Saskia Lassche; Tim Lavin; Carlo Marcelis; Peter Marks; Chiara Marini-Bettolo; Livija Medne; Ali-Reza Moslemi; Anna Sarkozy; Mary M Reilly; Francesco Muntoni; Francisca Millan; Colleen C Muraresku; Anna C Need; Andrea H Nemeth; Sarah B Neuhaus; Fiona Norwood; Marie O'Donnell; Mary O'Driscoll; Julia Rankin; Sabrina W Yum; Zarazuela Zolkipli-Cunningham; Isabell Brusius; Gilbert Wunderlich; Mert Karakaya; Brunhilde Wirth; Khalid A Fakhro; Homa Tajsharghi; Carsten G Bönnemann; Jenny C Taylor; Henry Houlden
Journal:  Brain       Date:  2021-03-03       Impact factor: 15.255

4.  Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.

Authors:  Nicholas M Pearce; Rachael Skyner; Tobias Krojer
Journal:  Front Mol Biosci       Date:  2022-04-11

5.  Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking.

Authors:  Marion Schuller; Galen J Correy; Stefan Gahbauer; Daren Fearon; Taiasean Wu; Roberto Efraín Díaz; Iris D Young; Luan Carvalho Martins; Dominique H Smith; Ursula Schulze-Gahmen; Tristan W Owens; Ishan Deshpande; Gregory E Merz; Aye C Thwin; Justin T Biel; Jessica K Peters; Michelle Moritz; Nadia Herrera; Huong T Kratochvil; Anthony Aimon; James M Bennett; Jose Brandao Neto; Aina E Cohen; Alexandre Dias; Alice Douangamath; Louise Dunnett; Oleg Fedorov; Matteo P Ferla; Martin Fuchs; Tyler J Gorrie-Stone; James M Holton; Michael G Johnson; Tobias Krojer; George Meigs; Ailsa J Powell; Victor L Rangel; Silvia Russi; Rachael E Skyner; Clyde A Smith; Alexei S Soares; Jennifer L Wierman; Kang Zhu; Natalia Jura; Alan Ashworth; John Irwin; Michael C Thompson; Jason E Gestwicki; Frank von Delft; Brian K Shoichet; James S Fraser; Ivan Ahel
Journal:  bioRxiv       Date:  2020-11-24

6.  Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.

Authors:  Marion Schuller; Galen J Correy; Stefan Gahbauer; Daren Fearon; Taiasean Wu; Roberto Efraín Díaz; Iris D Young; Luan Carvalho Martins; Dominique H Smith; Ursula Schulze-Gahmen; Tristan W Owens; Ishan Deshpande; Gregory E Merz; Aye C Thwin; Justin T Biel; Jessica K Peters; Michelle Moritz; Nadia Herrera; Huong T Kratochvil; Anthony Aimon; James M Bennett; Jose Brandao Neto; Aina E Cohen; Alexandre Dias; Alice Douangamath; Louise Dunnett; Oleg Fedorov; Matteo P Ferla; Martin R Fuchs; Tyler J Gorrie-Stone; James M Holton; Michael G Johnson; Tobias Krojer; George Meigs; Ailsa J Powell; Johannes Gregor Matthias Rack; Victor L Rangel; Silvia Russi; Rachael E Skyner; Clyde A Smith; Alexei S Soares; Jennifer L Wierman; Kang Zhu; Peter O'Brien; Natalia Jura; Alan Ashworth; John J Irwin; Michael C Thompson; Jason E Gestwicki; Frank von Delft; Brian K Shoichet; James S Fraser; Ivan Ahel
Journal:  Sci Adv       Date:  2021-04-14       Impact factor: 14.957

7.  Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics.

Authors:  Carlos G Acevedo-Rocha; Aitao Li; Lorenzo D'Amore; Sabrina Hoebenreich; Joaquin Sanchis; Paul Lubrano; Matteo P Ferla; Marc Garcia-Borràs; Sílvia Osuna; Manfred T Reetz
Journal:  Nat Commun       Date:  2021-03-12       Impact factor: 14.919

8.  Expanding the phenotypic spectrum of BCS1L-related mitochondrial disease.

Authors:  Omar Hikmat; Pirjo Isohanni; Nandaki Keshavan; Matteo P Ferla; Elisa Fassone; Mary-Alice Abbott; Marcello Bellusci; Niklas Darin; David Dimmock; Daniele Ghezzi; Henry Houlden; Federica Invernizzi; Nazreen B Kamarus Jaman; Manju A Kurian; Eva Morava; Karin Naess; Juan Darío Ortigoza-Escobar; Sumit Parikh; Alessandra Pennisi; Giulia Barcia; Karin B Tylleskär; Damien Brackman; Saskia B Wortmann; Jenny C Taylor; Laurence A Bindoff; Vineta Fellman; Shamima Rahman
Journal:  Ann Clin Transl Neurol       Date:  2021-10-18       Impact factor: 5.430

9.  Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

Authors:  Alice Douangamath; Daren Fearon; Paul Gehrtz; Tobias Krojer; Petra Lukacik; C David Owen; Efrat Resnick; Claire Strain-Damerell; Anthony Aimon; Péter Ábrányi-Balogh; José Brandão-Neto; Anna Carbery; Gemma Davison; Alexandre Dias; Thomas D Downes; Louise Dunnett; Michael Fairhead; James D Firth; S Paul Jones; Aaron Keeley; György M Keserü; Hanna F Klein; Mathew P Martin; Martin E M Noble; Peter O'Brien; Ailsa Powell; Rambabu N Reddi; Rachael Skyner; Matthew Snee; Michael J Waring; Conor Wild; Nir London; Frank von Delft; Martin A Walsh
Journal:  Nat Commun       Date:  2020-10-07       Impact factor: 14.919

  9 in total

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