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If the exploration targets are screened only using geological parameters, some resources that have superior geological conditions but little economic value may enter the exploration sequence and remain until their lack of economic value is shown.
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The progress achieved by several groups in the field of computational protein design shows that successful design methods include two major features: efficient algorithms to deal with the combinatorial exploration of sequence space and optimal energy functions to rank sequences according to their fitness for the given fold.
In principle, CPD can easily generate hundreds of thousands of sequences for a single backbone template, potentially improving the exploration of sequence space in cases where experimental data is rare.
Successful design methods should allow the exploration of sequence space not found in nature.
Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences.
Therefore, construction and testing of random domain insertion libraries, in which a host protein domain is randomly inserted into a guest protein domain, significantly benefit extensive exploration of sequence spaces for insertion sites.
DOI: http://dx.doi.org/10.7554/eLife.11282.015 Figure 4B offers an alternative perspective on the exploration of sequence space by the HIV-1 populations.
We expect that the systematic exploration of sequence space, the reproducible patterns of minor variation, and frequent reversion will be characteristic of other RNA viruses.
The reproducible exploration of sequence space can coexist with frequent adaptation only in frequently recombining large populations (Neher et al., 2013).
These mutations seem to be compatible with a stability-activity tradeoff that allows a broader exploration of sequence space by nature.
In the future, an in depth exploration of sequence diversity in S. sclerotiorum should allow to reveal more sites subjected to selection.
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