Intrinsically Disordered Protein: Difference between revisions
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* [http://www.pondr.com/ PONDR] (Dunker Group, Indiana University and Molecular Kinetics, Inc., Indianapolis IN USA; Obradovic Group, Temple Univ., Philadelphia PA USA). "PONDR® functions from primary sequence data alone. The predictors are feedforward neural networks that use sequence information from windows of generally 21 amino acids. Attributes, such as the fractional composition of particular amino acids or hydropathy, are calculated over this window, and these values are used as inputs for the predictor. The neural network, which has been trained on a specific set of ordered and disordered sequences, then outputs a value for the central amino acid in the window. The predictions are then smoothed over a sliding window of 9 amino acids. If a residue value exceeds a threshold of 0.5 (the threshold used for training) the residue is considered disordered." (Quoted from the PONDR website.) | * [http://www.pondr.com/ PONDR] (Dunker Group, Indiana University and Molecular Kinetics, Inc., Indianapolis IN USA; Obradovic Group, Temple Univ., Philadelphia PA USA). "PONDR® functions from primary sequence data alone. The predictors are feedforward neural networks that use sequence information from windows of generally 21 amino acids. Attributes, such as the fractional composition of particular amino acids or hydropathy, are calculated over this window, and these values are used as inputs for the predictor. The neural network, which has been trained on a specific set of ordered and disordered sequences, then outputs a value for the central amino acid in the window. The predictions are then smoothed over a sliding window of 9 amino acids. If a residue value exceeds a threshold of 0.5 (the threshold used for training) the residue is considered disordered." (Quoted from the PONDR website.) | ||
* [http://prodata.swmed.edu/Lab/Software.htm WinDiso]<ref>PMID: 17893360</ref> (Grishin Lab, Dallas, Texas USA). " | * [http://prodata.swmed.edu/Lab/Software.htm WinDiso]<ref>PMID: 17893360</ref> (Grishin Lab, Dallas, Texas USA). "WinDiso is a linear, sequence- and alignment-based predictor of disordered/unfolded regions in proteins. It has the capability of adjusting for the increased tendency for disorder at protein termini. The simple weighted window-based algorithm and careful optimization technique make this a good predictor to use when trying to avoid bias toward special cases." (Quoted from the Grishin lab website.) | ||
''The above list is incomplete. Addition of other servers is welcome, and summaries of methods, pros and cons for each server would be useful.'' | ''The above list is incomplete. Addition of other servers is welcome, and summaries of methods, pros and cons for each server would be useful.'' | ||