Steinbeck finds refinement and sensitivity where others might see only sniffing and peeing.
We found refinement to have little effect on the scoring of one-star structures (results not shown).
The general problem we address is the following: Given a non-binary gene tree G and a species tree S, find a refinement of G containing the minimum number of NADs with respect to S. Such a refinement of G is called a minimum refinement of G w.r.t. S. Hence, we aim at refining each non-binary node of G.
But this can be beneficial – to make something that at first is large and bold, and later find the refinement".
In some cases, as suggested by Nickles (1973) and Wimsatt (1976), the conception of strong analogy may find further refinement by appeal to what was referred to as the "physicist's" sense of reduction.
We previously found that refinement in HADDOCK does not systematically improve RMSD, but does result in significant improvements in the fraction of native contacts (fnat), if the structure is already of one-star quality [8].
Particles were rejected that were found after refinement to have changes in any of these parameters by more than 2σ.
The contrasts may be simple, perhaps obvious, and certainly there's venom, but it is the lyricism that lingers, and which would find its purest refinement in Vigo's third and final film, the luminous L'Atalante.
While SGD prioritizes addition of novel or missing annotations, other groups may find that annotation refinement is helpful, depending on their annotation philosophy.
We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single-molecule refinement.
