Predicting Disordered Regions from Amino Acid Sequence: Common Themes Despite Differing Structural Characterization
- PMID: 11072336
Predicting Disordered Regions from Amino Acid Sequence: Common Themes Despite Differing Structural Characterization
Abstract
Using ordered and disordered regions identified either by X-ray crystallography or by NMR spectroscopy, we trained neural networks to predict order and disorder from amino acid sequence. Although the NMR-based predictor initially appeared to be much better than the one based on the X-ray data, both predictors yielded similar overall accuracies when tested on each other's training sets, and indicated similar regions of disorder upon each sequence. The predictors trained with X-ray data showed similar results for a 5-cross validation experiment and for the out-of-sample predictions on the NMR characterized data. In contrast, the predictor trained with NMR data gave substantially worse accuracies on the out-of-sample X-ray data as compared to the accuracies displayed by the 5-cross validation during the network training. Overall, the results from the two predictors suggest that disordered regions comprise a sequence-dependant category distinct from that of ordered protein structure.
Similar articles
-
Predicting intrinsic disorder from amino acid sequence.Proteins. 2003;53 Suppl 6:566-72. doi: 10.1002/prot.10532. Proteins. 2003. PMID: 14579347
-
Predicting Protein Disorder for N-, C-, and Internal Regions.Genome Inform Ser Workshop Genome Inform. 1999;10:30-40. Genome Inform Ser Workshop Genome Inform. 1999. PMID: 11072340
-
Predicting Binding Regions within Disordered Proteins.Genome Inform Ser Workshop Genome Inform. 1999;10:41-50. Genome Inform Ser Workshop Genome Inform. 1999. PMID: 11072341
-
Intrinsic disorder in the Protein Data Bank.J Biomol Struct Dyn. 2007 Feb;24(4):325-42. doi: 10.1080/07391102.2007.10507123. J Biomol Struct Dyn. 2007. PMID: 17206849
-
Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered.J Theor Biol. 2008 Oct 21;254(4):799-803. doi: 10.1016/j.jtbi.2008.05.040. Epub 2008 Jun 14. J Theor Biol. 2008. PMID: 18611404
Cited by
-
Protein disorder prediction by condensed PSSM considering propensity for order or disorder.BMC Bioinformatics. 2006 Jun 23;7:319. doi: 10.1186/1471-2105-7-319. BMC Bioinformatics. 2006. PMID: 16796745 Free PMC article.
-
Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development.Int J Mol Sci. 2019 Oct 23;20(21):5260. doi: 10.3390/ijms20215260. Int J Mol Sci. 2019. PMID: 31652801 Free PMC article.
-
The N-terminal intrinsically disordered domain of Mgm101p is localized to the mitochondrial nucleoid.PLoS One. 2013;8(2):e56465. doi: 10.1371/journal.pone.0056465. Epub 2013 Feb 13. PLoS One. 2013. PMID: 23418572 Free PMC article.
-
Intrinsic disorder and functional proteomics.Biophys J. 2007 Mar 1;92(5):1439-56. doi: 10.1529/biophysj.106.094045. Epub 2006 Dec 8. Biophys J. 2007. PMID: 17158572 Free PMC article. Review.
-
Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. Protein Sci. 2016. PMID: 26683124 Free PMC article.