TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder.

By Andrew Campen, Ryan M. Williams, C. Brown, Jingwei Meng, Vladimir N Uversky, A. Keith Dunker. Protein Peptide Letters, 2008

387 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/326039a1c118807711eaefe8fe3d79e4d684cf78

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Citations in the corpus

Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions (2017, methodology): “It combines outputs of six predictors of intrinsic disorder: PONDR-VLXT [48], PONDR-VSL2 [52,53], PONDR-VL3 [50], FoldIndex [44], IUPred [46] and TopIDP [99], using a neural network.”
Using deep learning to annotate the protein universe (2019, background): “Most substitutions in the disordered region are predicted to have negligible e ﬀ ect, with the exception of mutations to phenylalanine, tyrosine and tryptophan, amino acids that are known to promote order [39].”
PONDR-FIT: A Meta-Predictor of Intrinsically Disordered Amino Acids (2010, background): “Similarly, by selecting the predictor which causes the minimal loss of accuracy at each step of reducing the number of component predictors, we may have the “slowest descent line” which is FoldIndex-VL3-VSL2-VLXT-TopIDP-IUPred.”
Intrinsically Disordered Proteins Studied by NMR Spectroscopy (2015, background): “While the signal that associated proline with IDP regions was evident but not particularly strong in this first study, later work with much larger datasets showed proline content to be a very strongly correlated with the presence of IDP regions (Campen et al. 2008; Theillet et al. 2013).”
Protein tandem repeats: the more perfect the less structured (2010, methodology): “Amino acids are arranged in order of decreasing structure-promoting ability as suggested by the TopIDP scale [37].”
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins (2010, background): “A specific amino-acid scale optimized to discriminate ordered and disordered regions was also constructed [66].”
A decade and a half of protein intrinsic disorder: Biology still waits for physics (2013, background): “Based on the analysis of 517 amino acid scales, a novel amino acid scale, Top-IDP (Trp, Phe, Tyr, Ile Met, Leu, Val, Asn, Cys, Thr, Ala, Gly, Arg, Asp, His, Gln, Lys, Ser, Glu, and Pro), was built to provide ranking for the tendencies of the amino acid residue to promote order or disorder.(30) The f”
Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis (2022, methodology): “The tendency of this long segment to possess disorder was further investigated by analyzing the amino acid composition using ExPASy ProtParam [37], which showed this region lacks order promoting residues C, L, F, W and Y [38] (Fig 1D).”