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Using the collected topology information, constrained predictions were made for all proteins in the database by HMMTOP (Tusnady and Simon, 1998; Tusnady and Simon, 2001) as well.
The distribution models of both techniques were coincident and congruent, although Maxent produced more constrained predictions than ENFA, highlighting the significantly better performance of the Maxent models for communities with fewer presences, in this study, black coral and brown garden eels.
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We constrained this behavior by instructing Maxent to use "clamping", a procedure which constrains predictions of environmental suitability so that environmental conditions that were not present in the training area do not produce extreme suitability estimates [49].
Yet, the approach of constraining predictions to within a pre-selected set of interactions limits the impact of these potential errors to related low-affinity complexes.
An expanded NAPSS algorithm, NAPSS-CS, is also provided that uses these spectroscopic properties to constrain predictions of RNA secondary structure.
Finally the SP-containing proteins were considered subdivided into soluble proteins and proteins containing TMHs, by assessing which proteins had TMHs predicted by a Phobius constrained prediction (constraint: N-terminus = signal peptide).
Topology data of the homologous proteins in the TOPDB database were used in the constrained prediction by mirroring their sequential positions according to the position of the HSPs.
The shoulder domain in the 2ZUO*b constrained prediction does look very similar to the MVP shoulder, which was identified as similar to the stomatin core of Pyrococcus horikoshii (Tanaka et al. 2009) (see fig. 6 insert).
Mutual information has been considered before in the context of experimental design for constraining predictions or parameters of interest [ 29], but not in the setting of model selection.
It is important to notice that in order to make it simple, we apply ROPE in its simple setting, where the motion estimation is evaluated at pixel level accuracy, and we use constrained intra prediction, so there are no error propagations in the intra prediction.
Furthermore, constrained intra prediction is applied, so there is no error propagation in the intra prediction.
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