Intrinsically Disordered Protein: Difference between revisions
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* [http://bip.weizmann.ac.il/fldbin/findex/ FoldIndex]<ref name="foldindex" /> makes predictions based on the observation that IUPs occupy the low hydrophobicity/ high net-charge portion of charge-hydrophobicity phase space. (See Figure above.) | * [http://bip.weizmann.ac.il/fldbin/findex/ FoldIndex]<ref name="foldindex" /> makes predictions based on the observation that IUPs occupy the low hydrophobicity/ high net-charge portion of charge-hydrophobicity phase space. (See Figure above.) | ||
* [http://iupred.enzim.hu/ IUPred] (Dosztányi, Csizmók, Tompa and Simon: Budapest, Hungary) "IUPred recognized intrinsically unstructured regions from the amino acid sequence based on the estimated pairwise energy content. The underlying assumption is that globular proteins are composed of amino acids which have the potential to form a large number of favorable interactions, whereas intrinsically unstructured proteins (IUPs) adopt no stable structure because their amino acid composition does not allow sufficient favorable interactions to form." (Quoted from the IUPred website.) | * [http://iupred.enzim.hu/ IUPred] (Dosztányi, Csizmók, Tompa and Simon: Budapest, Hungary). "IUPred recognized intrinsically unstructured regions from the amino acid sequence based on the estimated pairwise energy content. The underlying assumption is that globular proteins are composed of amino acids which have the potential to form a large number of favorable interactions, whereas intrinsically unstructured proteins (IUPs) adopt no stable structure because their amino acid composition does not allow sufficient favorable interactions to form." (Quoted from the IUPred website.) | ||
* [http://www.pondr.com/ PONDR] | * [http://www.pondr.com/ PONDR] | ||
* [http://prodata.swmed.edu/Lab/Software.htm WinDiso]<ref>PMID: 17893360</ref> "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.) | * [http://prodata.swmed.edu/Lab/Software.htm WinDiso]<ref>PMID: 17893360</ref> (Grishin Lab, Dallas, Texas USA). "WinDios 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.'' | ||
