Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors.

ABSTRACT: The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner,

SUBMITTER: Staritzbichler R 

PROVIDER: S-EPMC8087094 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature