Sentence examples for flexible alignments from inspiring English sources

Although, compared with the case with DaliLite, greater values of both sensitivity and precision, except for the quite low (5 10%) range of sequence identity, were observed using Fr-TM-align, which allows flexible alignments, for all matrices and methods, overall trends were preserved in both cases.

To assess the alignment quality, we compared sequence alignments with the structural alignments generated by Fr-TM-align (Pandit and Skolnick, 2008), which allows flexible alignments, and DaliLite (ver. 3.3) (Holm et al., 2008) as reference alignments.

Here, pharmACOphore is presented, a new approach for pairwise as well as multiple flexible alignments of ligands based on ant colony optimization (ACO) [1].

The method is based on flexible alignments using a new design paradigm and scoring system that aims to reduce the molecular weight of the compound and preferentially lead to drug like molecules.

For ligand based pharmacophore design, multiple flexible alignments of ligands was employed using PharmaGist [31].

A third method, which can handle flexible alignments, is the HingeProt [ 20] method.

Since these representative pairs involve domain movements, rigid alignment methods would not be able to align these pairs effectively, while flexible alignment methods will be able to introduce hinges and align the pairs more effectively.

Flexible alignment is correctly seen as an important innovation in aligning protein structures, however our results demonstrate that it is not a panacea: introducing flexibility into alignments greatly enlarges the search space, exacerbating problems in generating high quality alignments for more distantly related proteins.

The two main flexible alignment methods, FlexProt [ 11] and FATCAT [ 12], work by clustering (chaining) aligned fragment pairs (AFPs) and allowing flexibility while chaining, by introducing hinges (twists).

The findings highlight the need for flexible alignment of regulations and procedures across nations and organisations.

Molecular modeling study including flexible alignment; electrostatic, hydrophobic mappings; and pharmacophore prediction were performed.