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We could not find a secondary match for the D. melanogaster SPS2 in D. willistoni, suggesting that this protein is lost in this species.
The advantage of the classic matching algorithm is that it performs considerably faster than the secondary match algorithm in cases where a large number of ligand placements have been generated for preceding interactions of the theozyme.
PpSP32 emerged as a secondary match for the same protein gel band.
They were designed to minimize chances of a secondary match, and to be 3′ biased where possible.
For these lines, both the best overall match and the best secondary match were to one or both of the reported intercross background with alignment scores of 0.7 or greater (OB1xB3 had a slightly lower alignment score due to known contamination by Chinese Hamster Ovary feeder cells, personal communication from Rosann Farber, Additional file 1).
Similar(55)
Therefore the secondary matching algorithm was used to place the Lys, and during the matching process the torsion_B and torsion_AB parameters between candidate Lys rotamers and potential ligand placements were not evaluated.
San Francisco's secondary matches up well with the Giants' receiving corps.
Matches are presented as one main match and a few secondary matches.
Classic matching and secondary matching each have their own advantages and disadvantages.
Second, the secondary matching algorithm can also be used to find theozyme interactions between two side chains.
RosettaMatch can place the theozyme side chains through two algorithms: classic matching as introduced by Zanghellini et al. [6], and "secondary matching".
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