Sentence examples for based on structural alignment from inspiring English sources

Comparison of functionally important surfaces identified in pneumivirinae M2-1 and filoviridae VP30 core domains, based on structural alignment by secondary structure matching (shown as cartoons in A ). (B ) The core domain of HMPV M2-1 ishownwn as a white surface, and the interacting zinc finger and tetramerization helix are shown in grey cartoon.

However, most of methods based on structural alignment cannot be used to search structures against large database, since it has high computational complexity.

Based on structural alignment (Fig. 3b) of wild-type AbOPH and the mutant AbOPHI211A, the carboxyl group of Ile211 in the AbOPHI211A MP complex structure represents a motion of 1.2 Å compared with the AbOPH MP complex.

The corresponding segment of MEC-4 comprises 633 residues for subunit A. Sequence homology based on structural alignment for all residues is 16.4% (104/633) identity and 32% similarity.

A segment of 594 amino acid residues in UNC-8 corresponds to the sequence of 417 residues of 2QTS subunit A. Sequence homology based on structural alignment for these residues is, 17% identity and 30.5% similarity.

The initial sequence alignments were manually modified based on structural alignments and superimpositions of coordinates of the homologous GPCRs using DS3.5.

Since sequence alignments based on structural alignments have been long considered to be the gold standard, it is reasonable to expect that substitution matrices based on structural alignments can lead to better performance in detecting remote homologs.

Multiple alignments were constructed using the Kalign program [ 19] followed by manual adjustments based on structural alignments generated using MUSTANG [ 20].

In an additional experiment we add high-quality models based on structural alignments to the set, which allows Vorescore to improve the fold recognition rate by another 50%.

Ranked by sequence similarity based on structural alignments, the tetanus HCRn domain (PDB ID 1YYN) ranked first out of all known structures in the Protein Data Bank (%ID = 17.7).

All alignments of MHCI amino acid sequences were performed using ClustalX for initial analyses [ 94] and later manually curated based on structural aspects and alignment with tetrapod sequences.