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[jabaws.git] / website / prog_docs / 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