The program was constrained to maintain stereochemistry of the input structures but allowed to sample ring conformations.
At each level j, the scaling functions are defined as, begin{aligned} phi _j (x) = sum _{k in mathbb {Z}} a_k phi _{j-1} (2x - k), end{aligned} (4 and the wavelets are given by: begin{aligned} psi _j x) = sum _{k in mathbb {Z}} b_k phi _{j-1} (2x - k), end{aligned} (5 where x is the spatial coordinates and (a_k) and (b_k) are coefficients usually constrained to maintain basis orthogonality.
For the SKI and chemokine templates, the random sequences are constrained to maintain the conserved, native cysteines.
Local realignments were constrained to maintain the overlap between the secondary structure elements found in the MTase structures used as modeling templates, and predicted for HEN1.
Given the imbalanced nature of GS, the bootstrapping was constrained to maintain the same proportion of active versus inactive items as observed in the entire GS.
Local realignments were constrained to maintain the overlap between the secondary structure elements found in the template structures, and those predicted for the target.
The results of this study suggest that COG subunits are evolutionary constrained to maintain the interactions between each other, as well with other partners involved in vesicular trafficking, in order to preserve both the integrity and function of the complex.
On one hand, they must be constrained to maintain the structural integrity of the complex, presumably through the conservation of the residues that are involved in the interaction between subunits.
Previous bioinformatic analysis has shown that the amino acid substitutions in MatK across land plants are not random but constrained to maintain the chemical nature and presumed function of MatK [ 36].
Here, we use computer simulations of neutral protein evolution constrained to maintain the folding and misfolding stability of the native state in order to study the differences between the standard genetic code and seven naturally occurring variants concerning their effects on protein stability.
Furthermore, conserved motifs seem to be constrained to maintain not only location but also the exact sequence variant at each particular position (Table 3 and Fig. 6), as described previously in the case of binding sites for transcription factors envolved in early Drosophila development [ 21].
