BMRZ Webportal
UPLABEL
UPLABEL Webportal

This webportal is currently unavailable

UPLABEL (Unique Pair Labeling) is an algorithm for finding optimal labeling patterns for the backbone assignment of proteins that cannot be assigned by conventional methods. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), certain types of amino acids are labeled with 13C or/and 15N such that cross peaks between 13CO(i-1) and 15NH(i) result only for pairs of sequentially adjacent amino acids. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the protein sequence. It is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. The UPLABEL algorithm uses combinatorial optimization to find labeling patterns that maximize the number of unique pair assignments with a minimal number of samples. Various auxiliary conditions, such as labeled amino acid availability and price, previously known partial assignments and sequence regions of particular interest, can be taken into account when determining optimal amino acid type-specific labeling patterns. Usage of the UPLABEL software as implemented in the webportal is free to use (software License by Peter Güntert).


Input files and parameters
Sequence file (CYANA format .seq file) : Required!
Maximum number of samples (range 2-15) : Required! Invalid Format! Invalid Range! Invalid Range!
Maximum occurance of a pair (1 is unique) : Required! Invalid Format! Invalid Range! Invalid Range!
Number of iterations (range 100-10000) : Required! Invalid Format! Invalid Range! Invalid Range!
Seed (random number) for the calculation : Required! Invalid Format! Invalid Range! Invalid Range!

Select the amino acid residue(s) which should not be included into the labeling scheme :

ALA    ARG    ASN    ASP    CYS    GLN    GLU    GLY    HIS    ILE   
LEU    LYS    MET    PHE    PRO    SER    THR    TRP    TYR    VAL   

Optional region specific parameters
Label sets a score that indicates how desirable it is if a cerrtain region is included into the schedule. Marker enables the user to specify that part of the sequence can be distinguished from the rest with another experiment or seperate information. (format example: 1..10=10,14..40=7)

Label :
Marker :

Score weighting factor (range 0-200): Required! Invalid Format! Invalid Range! Invalid Range!

Optional amino acids price information
The price provides a measure for negative importance of a certain amino acid. (input range: 0-30000)

Amino acid : ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE
13C labeled :                              
15N labeled :                              
13C15N both :                              

Amino acid : LEU LYS MET PHE PRO SER THR TRP TYR VAL
13C labeled :                              
15N labeled :                              
13C15N both :                              

Price weighting factor (range 0-200): Required! Invalid Format! Invalid Range! Invalid Range!

Job Submission
This webportal is currently unavailable