RaaMLab: A MATLAB toolbox that generates amino acid groups and reduced amino acid modes

•RaaMLab offers four kinds of databases of amino acids’ on physicochemical properties and amino acid groupings.•RaaMLab offers 49 classification methods to reduce the amino acids.•RaaMLab offers five kinds of biophysciochemical features of the reduced amino acids. Amino acid (AA) classification and...

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Vydáno v:BioSystems Ročník 180; s. 38 - 45
Hlavní autoři: Xi, Baohang, Tao, Jin, Liu, Xiaoqing, Xu, Xinnan, He, Pingan, Dai, Qi
Médium: Journal Article
Jazyk:angličtina
Vydáno: Ireland Elsevier B.V 01.06.2019
Témata:
AA index
Algorithms
Amino acid
Amino Acids - chemistry
Biophysical Phenomena
Chemical Phenomena
Classification method
Computational Biology - methods
Internet
Peptides - chemistry
Protein features
Proteins - chemistry
Software
Classification method
Protein features
Amino acid
AA index
ISSN:0303-2647, 1872-8324, 1872-8324
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Shrnutí:•RaaMLab offers four kinds of databases of amino acids’ on physicochemical properties and amino acid groupings.•RaaMLab offers 49 classification methods to reduce the amino acids.•RaaMLab offers five kinds of biophysciochemical features of the reduced amino acids. Amino acid (AA) classification and its different biophysical and chemical characteristics have been widely applied to analyze and predict the structural, functional, expression and interaction profiles of proteins and peptides. We present RaaMLab, a free and open-source MATLAB toolbox, to facilitate studies on proteins and peptides, to generate AA groups and to extract the structural and physicochemical features of reduced AAs (RedAA). This toolbox offers 4 kinds of databases, including the physicochemical properties of AAs and their groupings, 49 AA classification methods and 5 types of biophysicochemical features of RedAAs. These factors can be easily computed based on user-defined alphabet size and AA properties of AA groupings. RaaMLab is an open source freely available at https://github.com/bioinfo0706/RaaMLab. This website also contains a tutorial, extensive documentation and examples.
Bibliografie:ObjectType-Article-1
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content type line 23
ISSN:0303-2647
1872-8324
1872-8324
DOI:10.1016/j.biosystems.2019.03.002