Assessment of disorder predictions in CASP8

Abstract

The interest in intrinsically disordered proteins has greatly increased, as it has become clear that they are very widespread, especially in eukaryotic organisms. Functionally, they appear to play a significant role in the control of many cellular processes and signalling pathways and have been, also, associated with a number of diseases ranging from cancer to Alzheimer's. Thus, there is enormous interest in attempts to predict disordered regions in proteins solely from knowledge of their amino acid sequences. In this study, we assess the quality of predictions for 25 groups on predicting disordered regions in 122 target proteins. In addition, we suggest the need of a “knowledge‐independent” measure that would enable one to normalize the results of the different CASP experiments and to determine whether the disorder prediction field had improved across the years. Proteins 2009. © 2009 Wiley‐Liss, Inc.

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

“…We did this by means of the disorder predictor VSL2 (31,32), which is one of the most precise predictors, according to the results of the last critical assessment of structure prediction rounds (33,34), with an accuracy of ϳ81% (32). We then classified each protein as ordered or disordered if more than 70% of its residues were predicted to be structured or unstructured, respectively.…”

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

“…PreDisorder (http://sysbio.rnet.missouri.edu/predis order.html) 139 was ranked among the best predictors in disorder prediction during CASP8 under the group name MULTICOM-CMFR. 140 The prediction is based on an ab initio neural network method. A PSI-BLAST profile of the sequence, along with the predicted secondary structure and solvent accessibility, is fed into a 1D Recursive Neural Network (1D-RNN) that forms the disorder predictions.…”

The Use of Refmac Crystallographic Refinement Program for Detection of Alternative Conformations in Biological Macromolecules

“…которое было предложено ранее для оценки результатов в соревновании CASP в секции «поиск разупорядоченных участков в белках» [17]. При использовании пороговых критериев достигаемая точность bACC зависит от выбранного значения порога.…”