FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4376278240> ?p ?o ?g. }

• W4376278240 abstract "Abstract Background Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity; however, this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences. Results We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity ( MorF : Mor pholog F inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in $${>}90%$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mo>></mml:mo> <mml:mn>90</mml:mn> <mml:mo>%</mml:mo> </mml:mrow> </mml:math> cases and annotates an additional $$50%$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mn>50</mml:mn> <mml:mo>%</mml:mo> </mml:mrow> </mml:math> of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF, and Ephrin signaling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. Conclusions Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this will be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms." @default.
• W4376278240 created "2023-05-13" @default.
• W4376278240 creator A5016012053 @default.
• W4376278240 creator A5018363483 @default.
• W4376278240 creator A5019985343 @default.
• W4376278240 creator A5038289093 @default.
• W4376278240 creator A5060933877 @default.
• W4376278240 creator A5065148584 @default.
• W4376278240 date "2023-05-12" @default.
• W4376278240 modified "2023-10-14" @default.
• W4376278240 title "Cross-phyla protein annotation by structural prediction and alignment" @default.
• W4376278240 cites W1596936080 @default.
• W4376278240 cites W1968045991 @default.
• W4376278240 cites W1970098795 @default.
• W4376278240 cites W1975304761 @default.
• W4376278240 cites W1976685063 @default.
• W4376278240 cites W1977075111 @default.
• W4376278240 cites W1978236589 @default.
• W4376278240 cites W1986099097 @default.
• W4376278240 cites W1988476050 @default.
• W4376278240 cites W1990453950 @default.
• W4376278240 cites W1993058298 @default.
• W4376278240 cites W1993393187 @default.
• W4376278240 cites W2002134090 @default.
• W4376278240 cites W2006531119 @default.
• W4376278240 cites W2011657487 @default.
• W4376278240 cites W2021033468 @default.
• W4376278240 cites W2025639892 @default.
• W4376278240 cites W2042301222 @default.
• W4376278240 cites W2045415864 @default.
• W4376278240 cites W2045534443 @default.
• W4376278240 cites W2050455566 @default.
• W4376278240 cites W2050987980 @default.
• W4376278240 cites W2053282269 @default.
• W4376278240 cites W2057021995 @default.
• W4376278240 cites W2062893328 @default.
• W4376278240 cites W2076048958 @default.
• W4376278240 cites W2091510848 @default.
• W4376278240 cites W2097270746 @default.
• W4376278240 cites W2101220662 @default.
• W4376278240 cites W2101692904 @default.
• W4376278240 cites W2110115297 @default.
• W4376278240 cites W2116000865 @default.
• W4376278240 cites W2122048837 @default.
• W4376278240 cites W2128049108 @default.
• W4376278240 cites W2132644745 @default.
• W4376278240 cites W2138122982 @default.
• W4376278240 cites W2138562686 @default.
• W4376278240 cites W2148471582 @default.
• W4376278240 cites W2149427712 @default.
• W4376278240 cites W2149653886 @default.
• W4376278240 cites W2155628349 @default.
• W4376278240 cites W2159803945 @default.
• W4376278240 cites W2165516561 @default.
• W4376278240 cites W2168172687 @default.
• W4376278240 cites W2173732482 @default.
• W4376278240 cites W2269834552 @default.
• W4376278240 cites W2301856115 @default.
• W4376278240 cites W2472351724 @default.
• W4376278240 cites W2478774501 @default.
• W4376278240 cites W2553676377 @default.
• W4376278240 cites W2595654377 @default.
• W4376278240 cites W2604973964 @default.
• W4376278240 cites W2785660739 @default.
• W4376278240 cites W2803453070 @default.
• W4376278240 cites W2804822363 @default.
• W4376278240 cites W2845591014 @default.
• W4376278240 cites W2895487334 @default.
• W4376278240 cites W2900629010 @default.
• W4376278240 cites W2941697941 @default.
• W4376278240 cites W2947226213 @default.
• W4376278240 cites W2949592035 @default.
• W4376278240 cites W2950030246 @default.
• W4376278240 cites W2950954328 @default.
• W4376278240 cites W2979523151 @default.
• W4376278240 cites W2989608901 @default.
• W4376278240 cites W3005171368 @default.
• W4376278240 cites W3006012565 @default.
• W4376278240 cites W3025857586 @default.
• W4376278240 cites W3095583226 @default.
• W4376278240 cites W3098880317 @default.
• W4376278240 cites W3104537585 @default.
• W4376278240 cites W3112376646 @default.
• W4376278240 cites W3127212423 @default.
• W4376278240 cites W3135108458 @default.
• W4376278240 cites W3139155037 @default.
• W4376278240 cites W3177828909 @default.
• W4376278240 cites W3178087467 @default.
• W4376278240 cites W3203343200 @default.
• W4376278240 cites W3210441301 @default.
• W4376278240 cites W3211795435 @default.
• W4376278240 cites W3215819479 @default.
• W4376278240 cites W4205731729 @default.
• W4376278240 cites W4206275111 @default.
• W4376278240 cites W4210840673 @default.
• W4376278240 cites W4220834327 @default.
• W4376278240 cites W4224257212 @default.
• W4376278240 cites W4281790889 @default.
• W4376278240 cites W4290928385 @default.
• W4376278240 cites W4303184143 @default.

• next