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A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method.

ABSTRACT: Alpha-helical transmembrane protein (?TMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of ?TMP are hard to be experimentally solved, but ?TMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted from topology structure and evolutionary information as features to implement a ?TMP Segment Alignment method (TMSA). The method was trained using one non-redundant dataset and tested using another non-redundant dataset. Comparing the results to a general alignment method HHalign, TMSA achieved higher alignment accuracy, and easier to recognize the fold of ?TMPs.

SUBMITTER: Wang H

PROVIDER: S-EPMC6036746 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method.

Wang Han H Wang Jingru J Zhang Li L Sun Pingping P Du Ning N Li Yanwen Y

International journal of biological sciences 20180522 8

Alpha-helical transmembrane protein (αTMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of αTMP are hard to be experimentally solved, but αTMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted ...[more]

PMID: 29989071

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