PoET single site analysis#
This tutorial shows you how to perform a single site analysis using PoET, which scores all single substitution variants of an input sequence with a given prompt. Use this as a starting point to design single mutant or combinatorial variant libraries and predict the strength of protein activity.
Find more information about the PoET model on our PoET API page.
What you need before getting started#
You need a prompt and a multiple sequence alignment (MSA). For more information, see Creating a multiple sequence alignment and Creating a prompt.
Running a single site analysis#
Run a single site mutation analysis of a sequence. This example uses KRAS:
[ ]:
poet = session.embedding.get_model("poet")
sspjob = poet.single_site(prompt=prompt, sequence="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM".encode())
Retrieve and view your results:
[ ]:
ssp_results = sspjob.wait()
ssp_results
{b'WT': array([-223.77676392, -225.38067627, -226.54772949]),
b'M1A': array([-227.33880615, -229.45011902, -229.57015991]),
b'M1R': array([-228.52160645, -229.91305542, -230.61193848]),
b'M1N': array([-227.66757202, -229.87303162, -229.40487671]),
b'M1D': array([-226.80749512, -228.89006042, -228.69639587]),
b'M1C': array([-228.81430054, -229.64477539, -230.38323975]),
b'M1Q': array([-228.05581665, -232.48745728, -232.58267212]),
b'M1E': array([-226.48562622, -229.09307861, -229.3104248 ]),
b'M1G': array([-228.62226868, -230.90753174, -231.29072571]),
b'M1H': array([-229.04473877, -232.14321899, -232.03407288]),
b'M1I': array([-227.21403503, -231.66772461, -230.8212738 ]),
b'M1L': array([-227.4931488 , -229.43362427, -229.17300415]),
b'M1K': array([-228.8396759 , -232.17623901, -231.95547485]),
b'M1F': array([-228.66670227, -231.17999268, -231.59490967]),
b'M1P': array([-227.80621338, -230.80247498, -230.60198975]),
b'M1S': array([-227.29650879, -229.75228882, -229.1946106 ]),
b'M1T': array([-227.57078552, -230.49655151, -230.46180725]),
b'M1W': array([-229.41436768, -231.41395569, -231.64422607]),
b'M1Y': array([-229.18579102, -232.92166138, -231.59947205]),
b'M1V': array([-229.59051514, -230.97636414, -231.72164917]),
b'T2A': array([-221.31245422, -224.3274231 , -224.76116943]),
b'T2R': array([-221.81555176, -222.99438477, -224.05119324]),
b'T2N': array([-223.54147339, -225.46389771, -226.00393677]),
b'T2D': array([-222.56515503, -225.15693665, -225.11973572]),
b'T2C': array([-223.5793457 , -225.47775269, -224.81362915]),
b'T2Q': array([-223.35150146, -224.38186646, -225.04208374]),
b'T2E': array([-220.23257446, -223.3059082 , -223.73945618]),
b'T2G': array([-220.69500732, -222.38449097, -223.12265015]),
b'T2H': array([-224.06260681, -226.45176697, -225.94781494]),
b'T2I': array([-223.95808411, -225.81414795, -226.17095947]),
b'T2L': array([-222.97894287, -224.93058777, -224.90730286]),
b'T2K': array([-222.59234619, -224.07397461, -224.63989258]),
b'T2M': array([-222.98345947, -224.94039917, -225.96749878]),
b'T2F': array([-224.04595947, -226.2313385 , -225.82229614]),
b'T2P': array([-223.22738647, -223.93652344, -225.57827759]),
b'T2S': array([-221.34965515, -223.29943848, -223.75115967]),
b'T2W': array([-225.0475769 , -226.0940094 , -226.35009766]),
b'T2Y': array([-225.0105896 , -226.94979858, -226.42893982]),
b'T2V': array([-220.63485718, -222.24014282, -222.56762695]),
b'E3A': array([-223.72964478, -226.41151428, -227.02633667]),
b'E3R': array([-224.49781799, -225.49287415, -227.11035156]),
b'E3N': array([-224.90135193, -226.11633301, -227.26397705]),
b'E3D': array([-223.61767578, -224.57479858, -226.09355164]),
b'E3C': array([-223.146698 , -227.25508118, -226.21136475]),
b'E3Q': array([-224.22969055, -224.95048523, -226.7543335 ]),
b'E3G': array([-222.56703186, -224.71768188, -225.83078003]),
b'E3H': array([-225.3840332 , -226.41567993, -227.72109985]),
b'E3I': array([-223.17044067, -225.5843811 , -226.79699707]),
b'E3L': array([-222.70925903, -225.12515259, -225.9909668 ]),
b'E3K': array([-224.77670288, -226.41238403, -227.8130188 ]),
b'E3M': array([-224.86726379, -227.58236694, -228.24377441]),
b'E3F': array([-223.8065033 , -227.11853027, -227.04922485]),
b'E3P': array([-224.51553345, -226.23762512, -227.4130249 ]),
b'E3S': array([-223.37257385, -225.67155457, -226.24716187]),
b'E3T': array([-224.61380005, -226.80374146, -227.9834137 ]),
b'E3W': array([-225.53085327, -227.71185303, -227.97465515]),
b'E3Y': array([-225.57568359, -228.27864075, -228.65682983]),
b'E3V': array([-222.37931824, -225.15023804, -225.86096191]),
b'Y4A': array([-220.67654419, -223.86529541, -223.19050598]),
b'Y4R': array([-218.0927887 , -223.49021912, -221.68534851]),
b'Y4N': array([-221.03900146, -228.08972168, -224.92901611]),
b'Y4D': array([-223.42863464, -231.91192627, -227.98582458]),
b'Y4C': array([-220.86096191, -223.46032715, -222.40744019]),
b'Y4Q': array([-218.97262573, -225.41488647, -223.08088684]),
b'Y4E': array([-220.89190674, -227.38845825, -224.83459473]),
b'Y4G': array([-224.00624084, -232.5211792 , -228.20541382]),
b'Y4H': array([-219.77311707, -223.39425659, -223.07452393]),
b'Y4I': array([-223.59344482, -227.44619751, -227.17207336]),
b'Y4L': array([-222.8918457 , -226.28692627, -225.83586121]),
b'Y4K': array([-218.90444946, -225.3678894 , -223.42463684]),
b'Y4M': array([-223.61624146, -227.91697693, -226.82794189]),
b'Y4F': array([-224.19468689, -226.52780151, -226.49725342]),
b'Y4P': array([-223.49240112, -228.71234131, -227.38581848]),
b'Y4S': array([-219.89942932, -225.27540588, -222.90158081]),
b'Y4T': array([-220.89332581, -225.63893127, -224.25071716]),
b'Y4W': array([-223.59448242, -227.40405273, -226.24780273]),
b'Y4V': array([-221.47525024, -225.13764954, -224.77755737]),
b'K5A': array([-228.64065552, -235.53507996, -234.57229614]),
b'K5R': array([-225.27020264, -226.50627136, -227.66932678]),
b'K5N': array([-225.76661682, -227.40953064, -228.56991577]),
b'K5D': array([-228.64053345, -232.35380554, -231.66555786]),
b'K5C': array([-228.28381348, -234.55401611, -232.62031555]),
b'K5Q': array([-224.8135376 , -226.34815979, -227.41326904]),
b'K5E': array([-225.78952026, -227.70718384, -228.06549072]),
b'K5G': array([-232.20770264, -242.35803223, -237.5977478 ]),
b'K5H': array([-226.51135254, -228.31192017, -229.12252808]),
b'K5I': array([-235.37010193, -249.37353516, -243.32476807]),
b'K5L': array([-234.37205505, -246.79756165, -241.50770569]),
b'K5M': array([-231.17279053, -237.75898743, -236.3717041 ]),
b'K5F': array([-236.28231812, -247.629776 , -242.69245911]),
b'K5P': array([-229.99099731, -239.15377808, -234.83132935]),
b'K5S': array([-224.46133423, -228.11503601, -228.13993835]),
b'K5T': array([-227.05870056, -230.87504578, -231.04386902]),
b'K5W': array([-230.84228516, -237.13594055, -235.62965393]),
b'K5Y': array([-229.08666992, -234.54013062, -233.94543457]),
b'K5V': array([-229.87915039, -238.42358398, -236.9286499 ]),
b'L6A': array([-221.73080444, -225.70518494, -224.87420654]),
b'L6R': array([-227.8927002 , -238.64326477, -233.61123657]),
b'L6N': array([-233.24687195, -247.19456482, -240.10844421]),
b'L6D': array([-243.104599 , -261.57382202, -253.78979492]),
b'L6C': array([-224.88253784, -227.35015869, -227.50247192]),
b'L6Q': array([-227.75793457, -236.42604065, -232.76774597]),
b'L6E': array([-237.02041626, -252.46922302, -245.10389709]),
b'L6G': array([-240.37780762, -261.3215332 , -250.0536499 ]),
b'L6H': array([-226.98342896, -232.16352844, -229.49026489]),
b'L6I': array([-225.80775452, -228.22087097, -228.77450562]),
b'L6K': array([-229.92288208, -244.09738159, -237.31350708]),
b'L6M': array([-225.07369995, -227.84391785, -227.09863281]),
b'L6F': array([-227.24313354, -228.65538025, -230.18099976]),
b'L6P': array([-232.86956787, -251.47264099, -241.11668396]),
b'L6S': array([-225.76690674, -233.83300781, -230.21183777]),
b'L6T': array([-224.55154419, -229.83093262, -227.85638428]),
b'L6W': array([-226.06472778, -229.44381714, -228.77856445]),
b'L6Y': array([-226.47113037, -227.6832428 , -228.71444702]),
b'L6V': array([-223.8130188 , -226.34182739, -226.74853516]),
b'V7A': array([-223.1010437 , -228.3918457 , -225.35720825]),
b'V7R': array([-230.91563416, -237.8862915 , -234.10090637]),
b'V7N': array([-227.57795715, -236.71551514, -230.3724823 ]),
b'V7D': array([-235.51260376, -246.16503906, -239.03001404]),
b'V7C': array([-224.12521362, -228.243927 , -227.0128479 ]),
b'V7Q': array([-228.27836609, -234.91145325, -231.12574768]),
b'V7E': array([-230.05239868, -235.93803406, -232.46902466]),
b'V7G': array([-224.69764709, -239.65969849, -231.36430359]),
b'V7H': array([-227.80728149, -233.60455322, -230.13873291]),
b'V7I': array([-225.96882629, -226.82620239, -228.25946045]),
b'V7L': array([-223.89482117, -226.11242676, -226.72746277]),
b'V7K': array([-229.65533447, -236.66540527, -233.23104858]),
b'V7M': array([-225.13807678, -228.35293579, -227.53752136]),
b'V7F': array([-226.80090332, -229.25357056, -228.75100708]),
b'V7P': array([-237.60238647, -247.01783752, -241.87567139]),
b'V7S': array([-225.03210449, -232.32199097, -227.75613403]),
b'V7T': array([-225.69839478, -231.11454773, -228.80384827]),
b'V7W': array([-228.97384644, -234.17483521, -231.31561279]),
b'V7Y': array([-228.65641785, -233.75109863, -231.46234131]),
b'V8A': array([-228.64398193, -230.93309021, -229.65917969]),
b'V8R': array([-235.83972168, -244.90805054, -239.92314148]),
b'V8N': array([-238.3270874 , -249.5446167 , -243.86483765]),
b'V8D': array([-268.93225098, -291.54312134, -281.73147583]),
b'V8C': array([-228.99575806, -232.53787231, -230.68191528]),
b'V8Q': array([-237.48110962, -243.84129333, -241.10725403]),
b'V8E': array([-237.95346069, -249.65690613, -244.38554382]),
b'V8G': array([-235.94168091, -243.31762695, -239.55775452]),
b'V8H': array([-236.41223145, -240.88897705, -238.85490417]),
b'V8I': array([-225.56765747, -227.67132568, -228.49191284]),
b'V8L': array([-227.30522156, -230.60144043, -230.39117432]),
b'V8K': array([-237.66770935, -249.79499817, -243.35302734]),
b'V8M': array([-230.77752686, -233.31448364, -233.15440369]),
b'V8F': array([-232.18598938, -237.12756348, -235.36978149]),
b'V8P': array([-240.67112732, -251.21736145, -245.35324097]),
b'V8S': array([-233.16708374, -235.15663147, -234.55509949]),
b'V8T': array([-231.22253418, -233.22869873, -232.28930664]),
b'V8W': array([-237.06282043, -240.4760437 , -239.27165222]),
b'V8Y': array([-238.01704407, -245.2164917 , -242.10394287]),
b'V9A': array([-222.80368042, -227.26368713, -226.17845154]),
b'V9R': array([-232.16304016, -240.01028442, -236.14639282]),
b'V9N': array([-232.44497681, -246.41989136, -237.88641357]),
b'V9D': array([-238.12789917, -250.18438721, -244.37701416]),
b'V9C': array([-219.60324097, -225.82800293, -223.2535553 ]),
b'V9Q': array([-234.09458923, -240.69837952, -240.35153198]),
b'V9E': array([-235.25485229, -239.54698181, -239.81359863]),
b'V9G': array([-242.82218933, -259.37435913, -249.45788574]),
b'V9H': array([-229.63273621, -236.25405884, -235.40971375]),
b'V9I': array([-226.01818848, -227.26179504, -228.49412537]),
b'V9L': array([-227.14907837, -229.66615295, -229.28787231]),
b'V9K': array([-235.27792358, -243.2182312 , -240.74752808]),
b'V9M': array([-226.25296021, -229.4066925 , -229.30583191]),
b'V9F': array([-225.47413635, -229.4987793 , -228.23025513]),
b'V9P': array([-240.06774902, -258.19921875, -247.39511108]),
b'V9S': array([-224.21421814, -233.56007385, -229.20257568]),
b'V9T': array([-224.91918945, -230.5891571 , -229.97555542]),
b'V9W': array([-227.35844421, -235.06660461, -230.02114868]),
b'V9Y': array([-224.19033813, -231.54536438, -227.93139648]),
b'G10A': array([-236.52857971, -249.15435791, -241.31541443]),
b'G10R': array([-306.24523926, -355.42346191, -326.83282471]),
b'G10N': array([-312.31970215, -360.98226929, -333.00341797]),
b'G10D': array([-379.01641846, -412.22189331, -400.56942749]),
b'G10C': array([-284.90979004, -323.23001099, -298.89007568]),
b'G10Q': array([-337.32858276, -377.81936646, -356.91461182]),
b'G10E': array([-299.29504395, -345.3223877 , -316.17611694]),
b'G10H': array([-370.53536987, -396.04223633, -383.30169678]),
b'G10I': array([-364.83294678, -398.04211426, -379.72033691]),
b'G10L': array([-385.69250488, -412.49520874, -399.25228882]),
b'G10K': array([-333.5249939 , -379.21282959, -353.83990479]),
b'G10M': array([-367.77972412, -404.14794922, -385.97906494]),
b'G10F': array([-365.38256836, -398.99432373, -379.76712036]),
b'G10P': array([-372.53201294, -403.11566162, -385.93222046]),
b'G10S': array([-241.55137634, -257.7199707 , -247.23202515]),
b'G10T': array([-285.95758057, -333.10632324, -302.25238037]),
b'G10W': array([-353.91577148, -382.52685547, -365.02593994]),
b'G10Y': array([-377.78826904, -403.9861145 , -388.39660645]),
b'G10V': array([-329.91821289, -372.11532593, -350.01983643]),
b'A11R': array([-225.85388184, -230.25790405, -228.99359131]),
b'A11N': array([-227.21884155, -229.40698242, -229.3699646 ]),
b'A11D': array([-232.58853149, -233.61416626, -232.26329041]),
b'A11C': array([-223.80194092, -227.10568237, -227.66363525]),
b'A11Q': array([-225.86082458, -229.1378479 , -227.66529846]),
b'A11E': array([-224.35073853, -226.76437378, -225.27252197]),
b'A11G': array([-224.03900146, -226.02404785, -225.4614563 ]),
b'A11H': array([-226.22253418, -227.29751587, -228.16177368]),
b'A11I': array([-225.49176025, -229.11872864, -228.94393921]),
b'A11L': array([-225.94979858, -229.24223328, -229.02839661]),
b'A11K': array([-229.9664917 , -235.55181885, -233.92268372]),
b'A11M': array([-224.41331482, -227.69137573, -227.13136292]),
b'A11F': array([-229.65344238, -232.86483765, -233.29498291]),
b'A11P': array([-227.62059021, -231.010849 , -230.48323059]),
b'A11S': array([-224.99467468, -226.79092407, -227.64944458]),
b'A11T': array([-224.15690613, -226.11239624, -227.12535095]),
b'A11W': array([-228.82913208, -233.18109131, -232.77790833]),
b'A11Y': array([-227.51881409, -229.80244446, -230.9940033 ]),
b'A11V': array([-223.15975952, -226.31182861, -226.5688324 ]),
b'G12A': array([-237.56396484, -242.05142212, -239.12524414]),
b'G12R': array([-239.72119141, -246.3821106 , -242.59333801]),
b'G12N': array([-250.33499146, -256.26037598, -251.78948975]),
b'G12D': array([-251.98916626, -256.3651123 , -253.67724609]),
b'G12C': array([-247.1305542 , -252.85333252, -248.86038208]),
b'G12Q': array([-243.95965576, -249.9178772 , -246.7901001 ]),
b'G12E': array([-241.20001221, -247.29312134, -244.69509888]),
b'G12H': array([-252.30184937, -259.10977173, -254.87606812]),
b'G12I': array([-255.78100586, -265.16943359, -258.98361206]),
b'G12L': array([-253.05136108, -260.25817871, -256.58355713]),
b'G12K': array([-242.00410461, -248.98364258, -246.03265381]),
b'G12M': array([-250.81031799, -258.17211914, -254.45608521]),
b'G12F': array([-260.85519409, -268.60015869, -263.6161499 ]),
b'G12P': array([-248.55111694, -255.40124512, -251.62677002]),
b'G12S': array([-245.39897156, -250.14427185, -246.40753174]),
b'G12T': array([-251.32984924, -256.66955566, -252.15682983]),
b'G12W': array([-251.96075439, -259.4072876 , -255.82104492]),
b'G12Y': array([-260.09417725, -268.58764648, -262.74996948]),
b'G12V': array([-246.54171753, -252.94500732, -248.72331238]),
b'G13A': array([-238.81047058, -241.20524597, -238.98617554]),
b'G13R': array([-243.33963013, -248.30479431, -245.77558899]),
b'G13N': array([-250.8515625 , -253.06053162, -252.65931702]),
b'G13D': array([-261.41876221, -263.79980469, -262.30090332]),
b'G13C': array([-250.59109497, -255.12168884, -252.03063965]),
b'G13Q': array([-249.20846558, -251.71078491, -250.73764038]),
b'G13E': array([-258.57232666, -259.86608887, -257.84225464]),
b'G13H': array([-263.16296387, -273.90966797, -268.246521 ]),
b'G13I': array([-405.63012695, -440.1237793 , -414.38189697]),
b'G13L': array([-322.42871094, -367.17736816, -337.01141357]),
b'G13K': array([-251.13874817, -256.24658203, -253.42074585]),
b'G13M': array([-296.08044434, -319.5057373 , -301.84106445]),
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b'L53G': array([-252.60105896, -253.73606873, -254.06851196]),
b'L53H': array([-256.34185791, -256.07580566, -257.7883606 ]),
b'L53I': array([-226.45819092, -227.78587341, -228.52932739]),
b'L53K': array([-307.58920288, -305.88381958, -309.90994263]),
...}
Because this is a Python dictionary, you can access specific site results:
[ ]:
ssp_results[b'D47C']
array([-244.84938049, -246.87284851, -247.89546204])
Next steps#
Now that you’ve scored your variants, you can plot and examine sites of interest to inform mutagenesis studies. To learn more, visit Understanding the impact of substitution and deletions on aliphatic amidase using different large language models.