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Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results.
However, while Goodman's index helpfully structures comparison of how national policies are conditioning entry, permanent residence and naturalization on language and civic knowledge, it arguably misses key developments in civic integration regimes adopted in Scandinavia and other countries, some of them implemented through family reunification policy.
Then, the learners were guided by an epitome statement that gave the instructional goals and objectives for each sub-lesson, relating to four sub-lessons (Anonymous 2000a): Logic patterns: (sequential, repetition and conditional control structures) Repetition logic: (using the DOWHILE and the REPEAT.. UNTIL structures) Comparison of the two logic patterns Example problems.
There is currently no agreement on a single method that is superior for protein structures comparison [ 8– 13].
Another method uses the second eigenvalue of the tree graph representation for the structures comparison, [ 15], and was later integrated into the RNAMute [ 16], a Java tool, which we will use for our second application illustration.
Pressing demand for computing power in the domain of protein structures comparison is the result of three factors: ever increasing size of structure databases [ 18], high computational complexity of PSC operations [ 19], and the trend towards applying multiple criteria PSC at a larger scale.
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Using Dali structure comparison method [39], the structural similarity between the FIV and the first four helices of EIAV Rev model structures was significant (CA RMSD = 2.8 Å).
In the structure comparison problem, determining the structural alignment of a protein pair is a fundamental step.
The 3-D superimposition of protein structures obtained by using structure comparison tools is very useful in quantifying structural dissimilarity and in analyzing structural divergence.
DaliLite is a widely used program for pairwise protein structure comparison and for deriving an optimal protein structural alignment.
Therefore, protein 3D structure comparison becomes an important tool to analyze structural divergence and in turn functional divergence.
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