NGL

Michelanglo — Documentation

Citation & licence


Relevant citation

Additionally, Michelaɴɢʟo and Venus depend on various other works. Most notably NGL:

Venus relies several datasets which are listed (with relevant publications) in the bottom of an analysis in the Venus page.

Typography and phonetics

Michelaɴɢʟo is a blend of Michelangelo —as in the sculptor not the ninja turtle— and NGL (the library that it uses) and as a consequence it can either be rendered in CamelCase MichelaNGLo or, preferably, with the NGL in small caps , thusly: Michelaɴɢʟo.

In terms of pronunciation, it is pronounced like the sculptor and it's your call if to pronounce with a terse first syllable /ˌmɪkəlˈændʒəloʊ/ (closer to Italian, albeit technically /mikeˈlandʒelo/) or a lax one /ˌmaɪkəlˈændʒəloʊ/ (as the ninja turtle calls himself) —the author of this site, despite speaking Italian, goes for the latter as it sounds less pretentious.

Licence

Michelaɴɢʟo

This site is open-source (see github.com/matteoferla/MichelaNGLo ) and released under the MIT licence. Any content within the user pages belongs to the creators and editors of those pages (therefore consult them for copyright/privacy etc.).

VENUS

VENUS (Variant Effect on Structure) itself is likewise open source under an MIT licence, but utilises several third party data, which are under different licences and as a result the page is for academic use only.

Specifically results concluded by data from a given databases should be acknowledged appropriately:

  • Specific crystal structure depends on the structure used. Not all deposited crystal structures have an associated paper. See relevant PDB entry for more.
  • Domain data is from Uniprot
    ??? License
    The UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47: D506-515 (2019).
  • Crystal structure data is from Protein Data Bank
    ? License
    H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
  • Phosphorylation data is from PhosphoSitePlus (R)
    Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License
    Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015 43:D512-20.
  • Kyle-Doolittle hydrophobicity scale
    Kyte, Jack; Doolittle, Russell F. (May 1982). "A simple method for displaying the hydropathic character of a protein". Journal of Molecular Biology. Elsevier BV. 157 (1): 105–32.
  • Human variability data is from gnomAD
    ? License
    Konrad J. Karczewski, Laurent C. Francioli, Grace Tiao, Beryl B. Cummings, Jessica Alföldi, Qingbo Wang, Ryan L. Collins, Kristen M. Laricchia, Andrea Ganna, Daniel P. Birnbaum, Laura D. Gauthier, Harrison Brand, Matthew Solomonson, Nicholas A. Watts, Daniel Rhodes, Moriel Singer-Berk, Eleanor G. Seaby, Jack A. Kosmicki, Raymond K. Walters, Katherine Tashman, Yossi Farjoun, Eric Banks, Timothy Poterba, Arcturus Wang, Cotton Seed, Nicola Whiffin, Jessica X. Chong, Kaitlin E. Samocha, Emma Pierce-Hoffman, Zachary Zappala, Anne H. O’Donnell-Luria, Eric Vallabh Minikel, Ben Weisburd, Monkol Lek, James S. Ware, Christopher Vittal, Irina M. Armean, Louis Bergelson, Kristian Cibulskis, Kristen M. Connolly, Miguel Covarrubias, Stacey Donnelly, Steven Ferriera, Stacey Gabriel, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Christopher Llanwarne, Ruchi Munshi, Sam Novod, Nikelle Petrillo, David Roazen, Valentin Ruano-Rubio, Andrea Saltzman, Molly Schleicher, Jose Soto, Kathleen Tibbetts, Charlotte Tolonen, Gordon Wade, Michael E. Talkowski, The Genome Aggregation Database Consortium, Benjamin M. Neale, Mark J. Daly, Daniel G. MacArthur. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv 531210.
  • Linear Motifs is from ELM database
    Academic License
    Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Res. 2018 Jan 4;46(D1):D428-D434.
  • Free energy calculations is from PyRosetta
    Academic License
    S. Chaudhury, S. Lyskov & J. J. Gray, "PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta," Bioinformatics, 26(5), 689-691 (2010).