propy swMATH ID: 22402 Software Authors: Cao, Dong - Sheng, Qing - Song Xu, Yi - Zeng Liang Description: propy: a tool to generate various modes of Chou’s PseAAC. 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. Homepage: https://www.ncbi.nlm.nih.gov/pubmed/23426256 Related Software: iRSpot-PseDNC; PseAAC-Builder; iSNO-PseAAC; Pse-in-One; PseAAC; iLoc-Hum; iRSpot-TNCPseAAC; iSNO-AAPair; PseAAC-General; iNuc-PseKNC; Cell-PLoc; PseKNC; iPPI-Esml; iPro54-PseKNC; iNuc-PhysChem; pSuc-Lys; iDNA-Methyl; iHyd-PseAAC; iAMP-2L; iLoc-Animal Cited in: 26 Documents all top 5 Cited by 62 Authors 6 Chou, Kuochen 5 Hayat, Maqsood 4 Xiao, Xuan 2 Ali, Farman 2 Brahnam, Sheryl 2 Du, Pufeng 2 Hussain, Waqar 2 Jia, Jianhua 2 Jiao, Ya-Sen 2 Khan, Sher Afzal 2 Khan, Yaser Daanial 2 Lumini, Alessandra 2 Nanni, Loris 2 Rasool, Nouman 1 Ahmad, Jamal 1 Arif, Muhammad 1 Bakhtiarizadeh, Mohammad Reza 1 Behbahani, Mandana 1 Biswas, Neela 1 Cao, Junzhe 1 Chen, Wei 1 Cheng, Xiang 1 Chong, Kil To 1 Dehzangi, Abdollah 1 Ding, Hui 1 Ebrahimi, Mansour 1 Ebrahimie, Esmaeil 1 Fan, Guoliang 1 Feng, Peng-Mian 1 Gu, Hong 1 Hajisharifi, Zohre 1 Huang, Chao 1 Jamil, Mehreen 1 Jan, Zahoor 1 Ju, Zhe 1 Khan, Muazzam Ali 1 Khan, Zaheer Ullah 1 Kumar, Ravindra 1 Kumari, Bandana 1 Li, Qianzhong 1 Li, Xiaoyan 1 Lin, Hao 1 Liu, Bingxiang 1 Liu, Zi 1 Lyons, James E. 1 Ma, Zhiqiang 1 Min, Jian-Liang 1 Mohabatkar, Hassan 1 Mohammad-Beigi, Majid 1 Mondal, Sukanta 1 Moradi-Shahrbabak, Mohammad 1 Ning, Qiao 1 Pai, Priyadarshini P. 1 Paliwal, Kuldip K. 1 Piryaiee, Moien 1 Qiu, Wangren 1 Sharma, Alok 1 Srivastava, Abhishikha 1 Tayara, Hilal 1 Wang, Pu 1 Yuan, Jingqi 1 Zhao, Xiaowei Cited in 2 Serials 25 Journal of Theoretical Biology 1 Computational & Mathematical Methods in Medicine Cited in 3 Fields 26 Biology and other natural sciences (92-XX) 8 Computer science (68-XX) 6 Statistics (62-XX) Citations by Year