Final refinement for alignment of gap regions was performed by generating 100 additional models, followed by selection of the best model on the basis of the ANOLEA score.
Refinement of the alignment closed gaps to produce agreement with labeling studies carried out on the homologous receptors of the superfamily.
Further refinement of the alignment was made manually.
In addition, we design a stochastic parallel framework that significantly speeds up the simultaneous refinement of multiple alignment candidates.
The FC values changed by <0.02 in all of the experiments, with the exception of the alignments of the CE and DM networks by GRAAL and PATH, where it increased by 0.024 and 0.027, respectively, as well as PISwap's refinement of their alignment by PATH, where it increased by 0.025.
Based on the above discussion, the 3-Opt technique performs a better refinement of global alignments of protein interaction networks, with only minimal time cost relative to the expensive initial alignment step.
Homology models were further obtained with Modeller version 6.2 [ 56] with additional refinement of structural alignments performed according to the Verify3D results as previously described [ 84].
Manual refinement of these alignments highlighted five additional unannotated introns in genes HOP2, CGI121, YPR170W-B, YPR153W, and YPL109C, of which only the HOP2 intron is present in S. cerevisiae (the HOP2 intron is not yet in SGD, but was recently described by Chan et al. [2014]).
To address this problem, in recent programs [ 4- 8] progressive alignment is usually preceded by consistency transformation (incorporating information from all pairwise alignments into the objective function) and/or followed by iterative refinement of the multiple alignment of all sequences.
After manual refinement of the sequence alignment, homology models of Cry8Ka1 (667 amino acid residues) and mutant Cry8Ka5 (649 amino acid residues) were created using MODELLER, Version 9.8 [ 37].
Compared with the refinement of the pairwise alignment of real PPI networks (the number of swaps required is 1960 and the improvement on EC ratio is 1.65% versus 9.6% for DM-SC), the refining effect is acceptable.
