|
Built from ideas by
Jaime Prilusky,
Tzviya Zeev-Ben-Mordehai,
Edwin Rydberg,
Clifford Felder,
Israel Silman and
Joel L. Sussman,
based on algorithm proposed by
Uversky VN, Gillespie JR, and Fink AL.
Why are "natively unfolded" proteins unstructured under physiologic
conditions?
Proteins 2000; 41:415-427.
In publications, credits should state:
FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded.
Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin Rydberg, Orna Man,
Jacques S. Beckmann, Israel Silman, and Joel L. Sussman, 2005, Bioinformatics.
(abstract ,
PDF).
|
|
FoldIndex© can be automatized:
FoldIndex can be used as a Web Service for remote and automatic data processing
by accessing this URL:
http://bioportal.weizmann.ac.il/fldbin/findex?m=xml&sq=SEQUENCE
where m is either xml or efam, as described below, and
sq is the one character code protein sequence, no spaces.
Here a simple working perl
script using this technique.
The server will send back the result the XML format requested by the user.
1. If the m (mode) parameter is set to xml, FoldIndex© will send back
the results in XML format (DTD, sample
XML).
2. If the m (mode) parameter is set to efam, FoldIndex© will send back
the results in
eFamily
compatible format.
Cross-referencing FoldIndex:
You may use either a UniProt or PDB id instead of a sequence for a
direct Cross-Reference to FoldIndex. These examples demonstrate how to
indicate the sequence to work on. You may combine this with any of the
other options (ie: eFam or xml output, window size):
sequence of chain B from PDB entry 2JBH
http://bip.weizmann.ac.il/fldbin/findex?sq=pdb:2jbh_b
sequence from UniProt P77990
http://bip.weizmann.ac.il/fldbin/findex?sq=uniprot:P77990
|