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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).
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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.
Brown, J., Collins, M., Tudhope, A. W. & Toniazzo, T. Modelling mid-Holocene tropical climate and ENSO variability: Towards constraining predictions of future climate change with palaeo-data.
The current lack of a comprehensive analysis of the capacity for physiological plasticity across taxonomic groups and geographic regions, however, constrains predictions of the impacts of climate change.
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.
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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