FoldIndex©

sequence
hydrophobicityKyte & Doolittle
window
step
Sequence area
graph's vertical scale
graph Phobic values
graph Charge values
show windows' verbose detail


FoldIndex© tries to answer to the question: Will this protein fold?
It's a dynamic and interactive process that estimates the local and general probability for the provided sequence, under specified conditions, to fold.
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

Server by
Jaime Prilusky, 2003-2006
Bioinformatics and Biological Computing
Israel Structural Proteomics Center
Weizmann Institute of Science