+++ /dev/null
- IUPred RELEASE NOTES
- ====================
-
-IUPred Version 1.0
-
-by Zsuzsanna Dosztanyi
-
-
-IUPred is supplied in source code form along with the required data files. The
-program is written in ANSI C and the code should compile on any ANSI C compiler
-e.g. the GNU C compiler. To be able to run outside the source directory, the
-IUPred_PATH environment variable has to be set to the location of the source
-files.
-
-TO COMPILE:
-
-cc iupred.c -o iupred
-
-TO RUN IUPred:
-
-iupred seqfile type
-
- where seqfile is the name of the sequence file
-
- type is any of the option of
-
- long
- short
- glob
-
- for prediction of long disorder, short disorder ( e.g. missing residues in
- X-ray structures) or predicting globular domains.
-
-
-INPUT FILE: sequence_file in fasta format. One sequence per file.
-
-EXAMPLE RUN:
-
-iupred P53_HUMAN.seq long
-
-
-INTERPRETATION OF THE OUTPUT:
-
-In the case of long and short types of disorder the output gives the
-likelihood of disorder for each residue, i.e. it is a value between 0 and 1,
-and higher values indicate higher probability of disorder. Residues with values
-above 0.5 can be regarded as disordered, and at this cutoff 5% of globular
-proteins is expected to be predicted to disordered (false positives).
-
-For the prediction type of globular domains it gives the number of globular
-domains and list their start and end position in the sequence. This is followed
-by the submitted sequence with residues of globular domains indicated by
-uppercase letters.
-
-
-Please see the LICENSE file for the license terms for the software. It is
-basically free for academic users, but a license fee applies to commercial
-users.
-
-THE PUBLICATION OF RESEARCH USING IUPred MUST INCLUDE AN APPROPRIATE
-CITATION TO THE METHOD:
-
-The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates
-between Folded and Intrinsically Unstructured Proteins
-Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon
-J. Mol. Biol. (2005) 347, 827-839.
-
-
-SHORT SUMMARY OF THE METHOD
-
-Intrinsically unstructured/disordered proteins have no single well-defined
-tertiary structure in their native, functional state. Our server recognizes
-such regions from the amino acid sequence based on the estimated pairwise
-energy content. The underlying assumption is that globular proteins make a
-large number of interresidue interactions, providing the stabilizing energy to
-overcome the entropy loss during folding. In contrast, IUPs have special
-sequences that do not have the capacity to form sufficient interresidue
-interactions. Taking a set of globular proteins with known structure, we have
-developed a simple formalism that allows the estimation of the pairwise
-interaction energies of these proteins. It uses a quadratic expression in the
-amino acid composition, which takes into account that the contribution of an
-amino acid to order/disorder depends not only its own chemical type, but also
-on its sequential environment, including its potential interaction partners.
-Applying this calculation for IUP sequences, their estimated energies are
-clearly shifted towards less favorable energies compared to globular proteins,
-enabling the predicion of protein disorder on this ground.
git://source.jalview.org / jabaws.git / blobdiff