AF6 PDZ domain - Prediction of dissociation constants for C-terminal ligands

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Sequence Input

To process a single C-terminus, please enter its sequence in one-letter code below and click 'Calculate Kd'.
Sequence
Only the last 4 residues are considered for calculation.

To process multiple C-termini, paste the raw sequences or a FASTA file in the input area below and click 'Calculate Multiple Kd'.


In case of a raw sequence file, place each sequence on a single line, FASTA files are interpreted as if each line containa a single C-terminal sequences.
Only the last 4 C-terminal positions will be used for the prediction. Sequences shorter than 4 residues are ignored.

AF6 Term Scheme

Specificity profile: Term Scheme



Dissociation constant calculation Output in [µM]

Mixed effects model without (no-IT) statistical pairwise interaction terms (R-square=0.72)
Kd [µM]    ln(Kd) (Column 2 below)
Prediction possible for all amino acids except for cysteine.

Fixed effects model with (w/-IT) statistical pairwise interaction terms (exp. validated R-square=0.76)
Kd [µM]    ln(Kd) (Column 3 below)
Prediction possible only for a reduced set of amino acids (see below).

For comparison only: Fixed effects model without (no-IT) statistical pairwise interaction terms (exp. validated R-square=0.67)
Kd [µM]    ln(Kd) (Column 4 below)
Prediction possible only for a reduced set of amino acids (see below).

As pointed out in the the paper (submitted), the prediction of the model including statistical interaction terms. Please use ONLY either the values of the mixed effects model or the fixed effects model including statistical interaction terms.

Calculation log
All your calculations will be summarized in the table below. The dissociation constants are given in [µM].
You can copy and paste the results and save them in an editor for future reference.

The fixed effects models are solely based on a single profile library.
The profile libraries are of the type bbbb(P-3)(P-2)(P-1)(P0)-COOH
For the AF6 profile library the positions P0 through P-3 were limited to the following sets of amino acids:

P0: V,I,L,F
P-1: L,I,D,E,N,Q,T,F,P,S,W,Y
P-2: F,I,L,S,T,V
P-3: A,E,D,F,G,P,S

The profile library therefore contained a total of 4x12x6x7 = 2016 peptides.
The mixed effects models included in addition to the profile library selected substitutional analyses. This analyses was thus based on a total of 3280 + 2016 = 5296 individual PDZ domain/peptide interaction measurements.

Reference:
Urs Wiedemann and Prisca Boisguerin, Rainer Leben, Dietmar Leitner, Gerd Krause, Karin Moelling, Rudolf Volkmer-Engert and Hartmut Oschkinat (2004) submitted.


Last modified: Tue May 18 23:09:55 W. Europe Daylight Time 2004

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