Matteo P Ferla1,2,3, Alistair T Pagnamenta1,2, David Damerell3, Jenny C Taylor1,2, Brian D Marsden3,4. 1. NIHR Oxford BRC, University of Oxford, Oxford, UK. 2. Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. 3. Structural Genomics Consortium, University of Oxford, Oxford, UK. 4. Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
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.
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.
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
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
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
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
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
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
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