A study on separation of the protein structural types in amino acid sequence feature spaces

Autoři: Xiaogeng Wan aff001;  Xinying Tan aff002
Působiště autorů: College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing, China aff001;  The Fourth Center of PLA General Hospital, Beijing, China aff002
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0226768


Proteins are diverse with their sequences, structures and functions, it is important to study the relations between the sequences, structures and functions. In this paper, we conduct a study that surveying the relations between the protein sequences and their structures. In this study, we use the natural vector (NV) and the averaged property factor (APF) features to represent protein sequences into feature vectors, and use the multi-class MSE and the convex hull methods to separate proteins of different structural classes into different regions. We found that proteins from different structural classes are separable by hyper-planes and convex hulls in the natural vector feature space, where the feature vectors of different structural classes are separated into disjoint regions or convex hulls in the high dimensional feature spaces. The natural vector outperforms the averaged property factor method in identifying the structures, and the convex hull method outperforms the multi-class MSE in separating the feature points. These outcomes convince the strong connections between the protein sequences and their structures, and may imply that the amino acids composition and their sequence arrangements represented by the natural vectors have greater influences to the structures than the averaged physical property factors of the amino acids.

Klíčová slova:

Machine learning – Protein sequencing – Protein structure – Protein structure databases – Sequence alignment – Sequence databases – Structural proteins – Vector spaces


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2019 Číslo 12
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