Also, our template interacting domain instances are from structurally resolved data in 3did, therefore the template domain instances are a relatively small number.
If good templates are found, the best covered domain is then modeled using a maximum of 2. Geno3D [ 29] (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling.
The secondary structure of the modelled TLR4 TIR domain is similar to that of the templates.
However, in our structure the OB domain is far away (∼40 Å) from the ssDNA overhang of the template strand.
All best scoring templates for the α1 domain were structures of HMG proteins.
Moreover, fold recognition servers, e.g., FFAS, predict the TPK catalytic domain being a good template for the COG1634 subunit fold; they also suggest even higher-scoring hits to the structures of bacterial GST-II-like sialyltransferases (Supplemental Figure 1).
9 Additionally, good resolution crystal structures of actin, tropomyosin and troponin core domain are used as templates to best-fit the cTF models.
Initially, homology model of the C-terminal regulatory domain was built using archeal CBS domain as a template (31).
The structure of Unsolved ORFs (or domains) is modeled according to our pipeline if a suitable template is available.
