BH-search
    To find potential membrane binding sites    		Help
    BH-search is a modified version of the EMBOSS pepinfo program that uses a modified hydrophibicity scale.
    It is designed to find potential membrane binding sites in proteins. More details in the following paper:
    An experimentally based computer search identifies unstructured membrane-binding sites in proteins:
    Application to class-I myosins, PAKs and CARMIL
    Hanna Brzeska, Jake Guag, Kirsten Remmert, Susan Chacko and Edward D. Korn J. Biol. Chem., 285: 5738-5747 (2010)

    Upload a file with one or more protein sequences:
    Sequence files must be in standard formats: Fasta, Genbank, Swissprot. More info

    OR Cut-and-paste one or more protein sequences into this box:
    Multi-sequence inputs must be in standard formats: Fasta, Genbank, Swissprot. More info
    Window size for residue averaging:

    Amino Acid Values:  use

    Define your own Amino Acid values

    The output from this run will include a parameter file that you can save and re-use for future runs.

    A: C: D: E:
    F: G: H: I:
    K: L: M: N:
    P: Q: R: S:
    T: V: W: Y:

    Upload a parameter file

    The parameter file must be in the correct format. It is best to do one run with 'Define your own parameters', save the parameter file from the output page, and then use the saved file for future runs.

    Upload a parameter file from your desktop:

    Sample sequences: (cut and paste the entire green section into the sequence box above) 
    >gi|24644586|ref|NP_731074.1| PAK-kinase, isoform C [Drosophila melanogaster]
MSSEEDKPPAPPVRLTSNRGGNERSGGGVGVGGGGLGGGGMGDVPPDMRPLPKEPDDSDRKKKTLKSKIK
GSKPSHTDSKPNISYPTNFEHTVHVGFDAVTGEFTGMPEAWARLLMNSNISKQEQKKNPQAVLDVLKWFD
NTTKQRPSSKYMTNAITTHSGSSLSRVSSSSPSSTPTDSELHGSNSGGNLIGVQLGSMTLGPNANNVAVA
GQILGNHYQQQQQHLLQQQQPLLHQNHNQHHMGISQSHSYNFVGHTVSSSTSQHSSANEDDMLGPQHPQQ
>gi|1359632|emb|CAA66660.1| p21 activated kinase [Entamoeba histolytica]
MVSCKKHGKTFWARRSLNIYNGLIALYAVNGEIPLTILPFSDNVEITKHQRLILIFQCVIRRVYLRFETE
EECNEVETLCKKCQQYYHKPQTMIVKDFFSGKLADLTPTCRELCNKNNLYPEECEKHFDTLCEILRSQTK
KRYATVTEKRQLQQKIRTSTSSYCFSKKRTSPEEDDLLRYCKTEEPHKYFTNLVSIGKGGFGEVFSLTQR
CFFFNPEERWSATQLLEHPFLKQADGSIIKQRGMKVGI

    Hanna Brzeska & Edward Korn (NHLBI), Susan Chacko (CIT)
    Email comments/problems to susan.chacko@nih.gov

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