Dear Ms. Sreetama Das,
you could select CA atoms of the secondary structure element you are
interested in,
create new pdb files with these atoms for each homologous, merge the
pdb files in
a single file in "dcd" format, so that to simulate a MD trajectory, run
vmd and
use the T-PAD tool [1] for determining the flexibility profile of the
ensamble of structures.
If interested, I can give you some useful scripts to performs such
calculations.
Best wishes,
Rocco
[1] Local Fluctuations and Conformational Transitions in Proteins
Caliandro et al. J. Chem. Theory Comput., 2012, 8 (11), pp 4775–4785
---
Dr. Rocco Caliandro, PhD
Istituto di Cristallografia (IC)
Consiglio Nazionale delle Ricerche (CNR)
via Amendola 122/o, 70126 Bari - Italy
Tel ++39 080 5929150
Fax ++39 080 5929170
mail: [log in to unmask]
web: users.ba.cnr.it/ic/crisrc25
Il 10/02/2016 8:54 sreetama das ha scritto:
> Dear All,
>
> I would like to compare the flexibility of the secondary structure
> elements forming the active site in homologous proteins. What are the
> possible methods of doing it? Not all the homologs have high sequence
> similarity (<50% similarity).
>
> I have looked at some older threads on the BB regarding usage of
> B-factors. While some have suggested the addition of a constant to the
> model with the lower B-factors to compare to the one with other
> B-factors, others have commented that it is not valid to compare
> B-factors for data collected from different crystals.
>
> Also, B-factor based-analysis can't be carried out when the homologs
> have NMR structures.
>
> Any suggestions? The tools may also include software/servers outside
> the CCP4 suite .
>
> Looking forward to your replies,
>
> Thanks and regards,
> Ms. Sreetama Das
>
> PhD student,
> Dept. of Physics,
> Indian Institute of Science
