[phenixbb] modelling a flexible peptide
faisaldbg at gmail.com
Tue Apr 3 18:43:10 PDT 2012
I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt
60 and 8 Kda respectively.
Molecular repalcement (60Kda protein as template) with Phaser gave a
solution with 6 molecules in ASU.
A continuous density is also obersved near two different chains which i
consider as the second protein.
I refined the density using a poly Alanine model but still i can't
recognise the side chains confidently for modelling.
Considering the fact that the smaller protein partner is rich in lysine,
arginine, Asp and Glutamate with only 3 tyr and 4 phe,
i tried to modell fragments one by one but the B-factor of the segments are
quite high (in the range of 110)
what will be the best strategy to improve the map for modelling.
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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