The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
propy: a tool to generate various modes of Chou’s PseAAC
Abstract
Summary: Sequence-derived structural and physiochemical features have been frequently used for analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate extensive studies of proteins and peptides, we developed a freely available, open source python package called protein in python (propy) for calculating the widely used structural and physicochemical features of proteins and peptides from amino acid sequence. It computes five feature groups composed of 13 features, including amino acid composition, dipeptide composition, tripeptide composition, normalized Moreau–Broto autocorrelation, Moran autocorrelation, Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors, composition, transition and distribution of various structural and physicochemical properties and two types of pseudo amino acid composition (PseAAC) descriptors. These features could be generally regarded as different Chou’s PseAAC modes. In addition, it can also easily compute the previous descriptors based on user-defined properties, which are automatically available from the AAindex database. Availability: The python package, propy, is freely available via http://code.google.com/p/protpy/downloads/list, and it runs on Linux and MS-Windows. Contact: yizeng_liang@263.net Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Some remarks on protein attribute prediction and pseudo amino acid composition
Chou, K.-C. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.12.024 · Cited by 1,225
Cited by
Liu, B., Liu, F., Wang, X., Chen, J., Fang, L., & Chou, K.-C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv458 · Cited by 721
Lin, H., Deng, E.-Z., Ding, H., Chen, W., & Chou, K.-C. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1019 · Cited by 508
Guo, S.-H., Deng, E.-Z., Xu, L.-Q., Ding, H., Lin, H., Chen, W., & Chou, K.-C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu083 · Cited by 375
Xiao, N., Cao, D.-S., Zhu, M.-F., & Xu, Q.-S. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv042 · Cited by 334
Self-citationLiu, B. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbx165 · Cited by 322
Metadata
- Authors
- Cao, D.-S., Xu, Q.-S., & Liang, Y.-Z.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-02-19
- Volume
- 29
- Issue
- 7
- Pages
- 960-962
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2160257187
- Cited by
- 476
- References
- 2
- FWCI
- 18.56
- Type
- journal article
- Language
- en
- Open access
- closed
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