Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / iupred / README

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+                       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.