getting rid of ambiguous documentation folder. all prog_doc are now stored in website...

[jabaws.git] / binaries / help / iupred.txt

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-INTERPRETATION OF THE OUTPUT:\r
-\r
-In the case of long and short types of disorder the output  gives the\r
-likelihood of disorder for each residue, i.e. it is a value between 0 and 1,\r
-and higher values indicate higher probability of disorder. Residues with values\r
-above 0.5 can be regarded as disordered, and at this cutoff 5% of globular\r
-proteins is expected to be predicted to disordered (false positives).\r
- \r
-For the prediction type of globular domains it gives the number of globular\r
-domains and list their start and end position in the sequence. This is followed\r
-by the submitted sequence with residues of globular domains indicated by\r
-uppercase letters. \r
-\r
-\r
-SHORT SUMMARY OF THE METHOD\r
-\r
-Intrinsically unstructured/disordered proteins have no single well-defined\r
-tertiary structure in their native, functional state. Our server recognizes\r
-such regions from the amino acid sequence based on the estimated pairwise\r
-energy content. The underlying assumption is that globular proteins make a\r
-large number of interresidue interactions, providing the stabilizing energy to\r
-overcome the entropy loss during folding. In contrast, IUPs have special\r
-sequences that do not have the capacity to form sufficient interresidue\r
-interactions. Taking a set of globular proteins with known structure, we have\r
-developed a simple formalism that allows the estimation of the pairwise\r
-interaction energies of these proteins. It uses a quadratic expression in the\r
-amino acid composition, which takes into account that the contribution of an\r
-amino acid to order/disorder depends not only its own chemical type, but also\r
-on its sequential environment, including its potential interaction partners.\r
-Applying this calculation for IUP sequences, their estimated energies are\r
-clearly shifted towards less favorable energies compared to globular proteins,\r
-enabling the predicion of protein disorder on this ground. \r
-\r
-       \r
-References\r
-\r
-"The Pairwise Energy Content Estimated from Amino Acid Composition \r
-Discriminates between Folded and Intrinsically Unstructured Proteins"\r
-Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon\r
-J. Mol. Biol. (2005) 347, 827-839.\r
-\r
-"IUPred: web server for the prediction of intrinsically unstructured \r
-regions of proteins based on estimated energy content"\r
-Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon\r
-Bioinformatics (2005) 21, 3433-3434.\r