Words similar to sequence-structure

Example sentences for: sequence-structure

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The sequence-structure threading with the 3D-PSSM method recovered the APSES domain structure (PDB 1bm8/1bm1) as the best hit for the Bro-N domain, albeit with statistically insignificant E-values.
As an example, a profile seeded with the MBP1p APSES domain and including all APSES domains in the NR database detects the N. meningitidis protein NMA1544 (gi:11290039) with an E-value of 0.1 in iteration 3. Given the availability of the three-dimensional structure of the APSES domain of the MBP1p protein [ 16, 17], we investigated this potential relationship using the KilA-N domain sequences for sequence-structure threading of the PDB database with the 3DPSSM, PSIPRED and combined-fold prediction algorithms.
Among the many sequence-structure features of JEvTrace is the ability to highlight the residues in contact with a selected position, using a residue-residue distance calculation and a distance cutoff.
Furthermore, methods based on a different principle, such as protein sequence-structure threading, have a recent history of success despite uncertainties in their statistical foundations [ 22, 53, 54, 55, 56].
A similar secondary structure pattern is also observed in several other ligand-binding domains such as the PAS, GAF, profilin and probably even the CACHE domains [ 10 ] . Sequence-structure threading using the 3DPSSM method detected the PAS domain (Photoactive yellow protein PDB: 1drm) with marginally significant scores (.5, 50-70% probability of correct fold prediction).