Dear Modellers,
I have used MODELLER to create 100 11-residue long loop models. Some of models
cannot form proper loops, so I used their objective function value as cut-off
to select loop models. However further biological structure-function studies of
the selected models are not all consistent with the experiment results in
vitro. Presumbaly, therefore, some of loop models shouldnot have been
selected. Meanwhile I threw the crystal structure of the template into MODELLER
to model the loop region, which is the corresponding position in the target
model. The loop redefinement of the crystal structure show very similar
conformations distribution to the model protein. In the crystal structure, 3
H-bonds stabilise the loop conformation. They are E-R , E-S. However R and S
are replaced by P and T in the model sequence.
So my questions is what the proper criteria is for this case? Should the
conservation of the H-bonds be checked in the loop models? If it is a way how
to check H-bonds in 100 loop models automatically before I have some ideas to
write a piece of program myself?
Many thanks for hints.
Binbin