However, to accommodate domain-dependent definitions, for which standardized ontologies may not exist, BioDEAL provides ways to extend the supported ontologies.
Consequently, there is a cap as proteomes have a finite space to accommodate domains (and their variants) and this space is "canalized" in evolution.
This could reflect a binding either to the blunt ends or to the duplex itself, which corresponds in size to the footprint of the F2 domain on a SSB (i.e. 7 bp on either side of the break) [21] and should therefore be able to accommodate this domain.
The structure of the prosurvival BCL-XL monomer revealed that its BH1, BH2, and BH3 domains are in close proximity and create a hydrophobic pocket that can accommodate a BH3 domain of the BAK proapoptotic member.
Since Membrane Builder determines the system size in XY only based on the size of the transmembrane domain, the system size generated by the default "1.5 lipid layers" was not big enough to accommodate the cellular domain.
Since a water molecule cannot accommodate its coordination domain inside a sub-nanoscale cavity, water effectively distances itself from exposed BHBs to a larger extent than from well protected bonds.
This effect was only evident with WT, but not L78A BAK, implying the requirement of an intact receptor surface to accommodate the BH3 domain of the activators.
In the future, transferring unconventional integrated domains to the different positions within and between NLRs will determine the importance of domain location, and whether these positions can accommodate novel integrated domains with the potential to deliver new-to-nature resistance capabilities.
Other key advantages include, being independent of underlying physical models (e.g., either FEM or meshless methods), being flexibly accommodating sub-domains' heterogeneous material distributions, and being accurately responding to local user interactions.
Although NRP2B antibody was originally developed to target the coagulation V/VII factor (b1-b2) domains of NRP2 which are required for VEGF-C binding to NRPs [ 21], and the b1-b2 domains do not directly engage SEMA, this antibody could decrease SEMA binding by preventing NRP dimerization that is necessary for accommodating SEMA domains that pack tightly together at this interface [ 57].
