%0 Journal Article
%T Length-dependent prediction of protein intrinsic disorder
%A Kang Peng
%A Predrag Radivojac
%A Slobodan Vucetic
%A A Keith Dunker
%A Zoran Obradovic
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-208
%X We proposed two new predictor models, VSL2-M1 and VSL2-M2, to address this length-dependency problem in prediction of intrinsic protein disorder. These two predictors are similar to the original VSL1 predictor used in the CASP6 experiment. In both models, two specialized predictors were first built and optimized for short (¡Ü30 residues) and long disordered regions (>30 residues), respectively. A meta predictor was then trained to integrate the specialized predictors into the final predictor model. As the 10-fold cross-validation results showed, the VSL2 predictors achieved well-balanced prediction accuracies of 81% on both short and long disordered regions. Comparisons over the VSL2 training dataset via 10-fold cross-validation and a blind-test set of unrelated recent PDB chains indicated that VSL2 predictors were significantly more accurate than several existing predictors of intrinsic protein disorder.The VSL2 predictors are applicable to disordered regions of any length and can accurately identify the short disordered regions that are often misclassified by our previous disorder predictors. The success of the VSL2 predictors further confirmed the previously observed differences in amino acid compositions and sequence properties between short and long disordered regions, and justified our approaches for modelling short and long disordered regions separately. The VSL2 predictors are freely accessible for non-commercial use at http://www.ist.temple.edu/disprot/predictorVSL2.php webciteIntrinsically disordered, or natively unfolded, proteins or protein regions do not fold into stable three dimensional (3-D) structures under physiological conditions; they instead exist as ensembles of non-cooperatively interchanging conformations in which the atom coordinates and backbone Ramachandran angles vary significantly over time with no specific equilibrium values [1-5]. Although lacking specific 3-D structures, many intrinsically disordered proteins/regions have been identifi
%U http://www.biomedcentral.com/1471-2105/7/208