Package: amphipathic
amphipathicThis library can analyze an aminoacid sequence and gives a list of secondary structures with the respective hydrophobicity mean[1] and amphipathic index[1].When it is useful to calculate this measurements on a secondary structure?By looking into this measurements for an alpha helix, you can test some hiphotesis related with:the context of aglobular soluble protein:hydrofobic core, it will be no amphipathic and hydrophobicinterface between core and the superficial region, it will be amphiphaticsuperficial region, it will be no amphipathic and hydrophilicthe interactions of atrans-membrane protein:on lipids interaction, it will be not amphipathic and hidrophobicon multiple trans-membrane helix interacion(homomeric or heteromeric), it will be amphipathic building like anionic channel.RequirementsIf you want to use this library on any GNU/Linux or OSX system you just need to execute:$ pip install amphipathicIf you want to collaborate with this library, you should download thegithub repositoryand execute:$ make deployTestingTo test all the project you should use the command:$ pytest testsExampleThis library can analyze an aminoacid sequence and gives a list of secondary structures with the respective hydrophobicity mean and amphipathic index.importamphipathicresume=amphipathic.index('NLYIQWLKDGGPSSGRPPPS')printresumeor specifingscale="prift"from Cornette et al.[1]importamphipathicresume=amphipathic.index('NLYIQWLKDGGPSSGRPPPS',scale="prift")printresumeAnd the result should be:[[{'end':2,'begin':0,'type':u'c','seq':'nl','amphipathic':{'index':7.572935321054872e-05,'mean':2.6}},{'end':5,'begin':2,'type':u'e','seq':'yiq','amphipathic':{'index':1.4312912272216411,'mean':1.7299999999999998}},{'end':18,'begin':5,'type':u'c','seq':'wlkdggpssgrpp','amphipathic':{'index':0.002511560979331271,'mean':-0.43}},{'end':20,'begin':18,'type':u'e','seq':'ps','amphipathic':{'index':1.6242872515167746,'mean':-1.34}}]]Each secondary structure block has specific information like:typecould be "c" (from coil), "e" (extended/beta sheet) or "h" (alpha helix).meanprovides the hydrophobicity mean obtained using the aminoacids of the block through Hydrophobicity scales obtained from Table 4 (STA PRIFT **) Cornette et al.[1].indexprovides an amphipathic index adapted from Cornette et al.[1], first implemented into Pablo Daniel Ghiringhelli's PhD thesis[2]. Cornette et al.[1] suggests an scalar equal or greater than 2, means apmhipathicity. On alpha helix cases this is only valid for segments shorter than 20-25 residues. When an alpha helix go further in longitude, the index is not valid anymore.It also accept a nucleotide sequence to perform the same analysis:importamphipathicresume=amphipathic.index('cgcgtccttggagcaatgcagttcaagaccaagaatcgaattgaacctgt')printresumeAnd the output:[[{'end':12,'begin':0,'type':u'c','seq':'rvlgamqfktkn','amphipathic':{'index':0.007560225956225585,'mean':0.7825000000000001}},{'end':15,'begin':12,'type':u'e','seq':'rie','amphipathic':{'index':1.6297837670649824,'mean':1.4599999999999997}},{'end':16,'begin':15,'type':u'c','seq':'p','amphipathic':{'index':0.0,'mean':-2.23}}]]Last, it also accept a polyprotein sequence. When working with aminoacid it detect the '*' character as a stop signal:importamphipathicresume=amphipathic.index('NLYIQWLKDG*GPSSGRPPPS')printresumeUsagesThis library was used intomistic2.Bibliography[1] Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., & DeLisi, C. (1987). Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. Journal of Molecular Biology, 195(3), 659–685. doi:10.1016/0022-2836(87)90189-6.[2] Ghiringhelli D (2002). Virus Junín: Clonado molecular y análisis estructural y funcional del RNA S y sus productos génicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata.Questions?If you want to develope with us or have questions about this library, please file an issue in this repository so some of the project managers can get back to you. Please check the existing (and closed) issues to make sure your issue hasn't already been addressed.