Sequence complexity of disordered protein

By Pedro Romero, Zoran Obradovic, Xiaohong Li, Ethan C. Garner, C. Brown, A. Keith Dunker. 2001

1,709 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning (2019, methodology): “JRONN [67], IUPred optimized for short and long disorder [IUpred (short)] and [IUpred (long)] [15], and PONDR-VSL [14] are not discussed here because of lower performance except the second-best shown below.”
Intrinsically unstructured proteins and their functions (2005, background): “A signature of probable intrinsic disorder is the presence of low sequence complexity and amino-acid compositional bias, with a low content of bulky hydrophobic amino acids (Val, Leu, Ile, Met, Phe, Trp and Tyr), which would normally form the core of a folded globular protein, and a high proportion ”
Flavors of protein disorder (2003, methodology): “Our data set of proteins with disordered regions longer than 30 consecutive residues was derived from a previously described data set.(24) Briefly, reports on disordered regions identified by NMR, circular dichroism, or protease digestion were located by keyword searches of PubMed (http://www.”
Intrinsic protein disorder in complete genomes. (2000, methodology): “The inputs were attributes such as hydropathy or compositions of certain amino acids calculated as simple averages over windows of 21 residues for VL1 [ 31 ] and over windows of various lengths for the two XTs [23].”
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling (2005, methodology): “…bulky hydrophobic amino acids (Val, Leu, Ile, Met, Phe, Trp and Tyr), which would normally form the core of a folded globular protein, and a high proportion of particular polar and charged amino acids (Gln, Ser, Pro, Glu, Lys and, on occasion, Gly and Ala Romero et al., 2001; Vucetic et al., 2003).”
Length-dependent prediction of protein intrinsic disorder (2006, methodology): “The amino acid compositions of short (4–30 residues) and long (>30 residues) disordered regions were compared to the composition of a reference ordered dataset, Globular-3D [18].”
Intrinsic disorder in cell-signaling and cancer-associated proteins. (2002, positive): “These data suggest that cytoskeletal proteins are indeed richer in coiled coils as compared to the other two categories, and that coiled coils are often predicted to be disordered by PONDR VL-XT.”
Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life (2012, background): “…Romero, Dunker, Brown, & Obradovic, 1999; Oldfield, Cheng, Cortese, Romero, et al., 2005), a disorder predictor which applies various compositional probabilities and hydrophobic measures of amino acid as the input features of artificial neural networks for the prediction (Romero et al., 2001).”
Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies (2015, methodology): “Two methods that use this approach are DISOPRED [36] and PONDR [26].”
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, methodology): “Methods PONDRs VL-XT and VSL1 Predictions of intrinsic disorder in HPV proteins were performed using a set of PONDR® (Predictor Of Natural Disordered Regions) predictors, VL-XT and VSL2.”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, background): “It has previously been observed that disordered proteins have a Shannon entropy (a measurement of sequence complexity) that is lower, but significantly overlapping with ordered proteins (Romero et al., 2001).”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, methodology): “The amino acid composition analysis was performed as previously described [22].”