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Repo setup (#1)
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* Adding notebooks and essential data to run the main analysis notebook

* Include gnomAD ACE2 variants VCF

* Include VCF index

* Include required proteofav output and the proteofav notebook that generates it

* Add mCSM-PPI2 submission lists

The folder is required for the main notebook and I might as well add the output to vcs.

* Add SARS-CoV ACE2 validation mutant assay data
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@stuartmac
stuartmac authored Apr 29, 2020
1 parent f597376 commit 062a2a4
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20,349 changes: 20,349 additions & 0 deletions ACE2-variants-structure-and-assays.ipynb
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35 changes: 35 additions & 0 deletions ACE2_CDS.fa
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>CDS|ENST00000427411/1-2415
ATGTCAAGCTCTTCCTGGCTCCTTCTCAGCCTTGTTGCTGTAACTGCTGCTCAGTCCACCATTGAGGAACAG
GCCAAGACATTTTTGGACAAGTTTAACCACGAAGCCGAAGACCTGTTCTATCAAAGTTCACTTGCTTCTTGG
AATTATAACACCAATATTACTGAAGAGAATGTCCAAAACATGAATAATGCTGGGGACAAATGGTCTGCCTTT
TTAAAGGAACAGTCCACACTTGCCCAAATGTATCCACTACAAGAAATTCAGAATCTCACAGTCAAGCTTCAG
CTGCAGGCTCTTCAGCAAAATGGGTCTTCAGTGCTCTCAGAAGACAAGAGCAAACGGTTGAACACAATTCTA
AATACAATGAGCACCATCTACAGTACTGGAAAAGTTTGTAACCCAGATAATCCACAAGAATGCTTATTACTT
GAACCAGGTTTGAATGAAATAATGGCAAACAGTTTAGACTACAATGAGAGGCTCTGGGCTTGGGAAAGCTGG
AGATCTGAGGTCGGCAAGCAGCTGAGGCCATTATATGAAGAGTATGTGGTCTTGAAAAATGAGATGGCAAGA
GCAAATCATTATGAGGACTATGGGGATTATTGGAGAGGAGACTATGAAGTAAATGGGGTAGATGGCTATGAC
TACAGCCGCGGCCAGTTGATTGAAGATGTGGAACATACCTTTGAAGAGATTAAACCATTATATGAACATCTT
CATGCCTATGTGAGGGCAAAGTTGATGAATGCCTATCCTTCCTATATCAGTCCAATTGGATGCCTCCCTGCT
CATTTGCTTGGTGATATGTGGGGTAGATTTTGGACAAATCTGTACTCTTTGACAGTTCCCTTTGGACAGAAA
CCAAACATAGATGTTACTGATGCAATGGTGGACCAGGCCTGGGATGCACAGAGAATATTCAAGGAGGCCGAG
AAGTTCTTTGTATCTGTTGGTCTTCCTAATATGACTCAAGGATTCTGGGAAAATTCCATGCTAACGGACCCA
GGAAATGTTCAGAAAGCAGTCTGCCATCCCACAGCTTGGGACCTGGGGAAGGGCGACTTCAGGATCCTTATG
TGCACAAAGGTGACAATGGACGACTTCCTGACAGCTCATCATGAGATGGGGCATATCCAGTATGATATGGCA
TATGCTGCACAACCTTTTCTGCTAAGAAATGGAGCTAATGAAGGATTCCATGAAGCTGTTGGGGAAATCATG
TCACTTTCTGCAGCCACACCTAAGCATTTAAAATCCATTGGTCTTCTGTCACCCGATTTTCAAGAAGACAAT
GAAACAGAAATAAACTTCCTGCTCAAACAAGCACTCACGATTGTTGGGACTCTGCCATTTACTTACATGTTA
GAGAAGTGGAGGTGGATGGTCTTTAAAGGGGAAATTCCCAAAGACCAGTGGATGAAAAAGTGGTGGGAGATG
AAGCGAGAGATAGTTGGGGTGGTGGAACCTGTGCCCCATGATGAAACATACTGTGACCCCGCATCTCTGTTC
CATGTTTCTAATGATTACTCATTCATTCGATATTACACAAGGACCCTTTACCAATTCCAGTTTCAAGAAGCA
CTTTGTCAAGCAGCTAAACATGAAGGCCCTCTGCACAAATGTGACATCTCAAACTCTACAGAAGCTGGACAG
AAACTGTTCAATATGCTGAGGCTTGGAAAATCAGAACCCTGGACCCTAGCATTGGAAAATGTTGTAGGAGCA
AAGAACATGAATGTAAGGCCACTGCTCAACTACTTTGAGCCCTTATTTACCTGGCTGAAAGACCAGAACAAG
AATTCTTTTGTGGGATGGAGTACCGACTGGAGTCCATATGCAGACCAAAGCATCAAAGTGAGGATAAGCCTA
AAATCAGCTCTTGGAGATAAAGCATATGAATGGAACGACAATGAAATGTACCTGTTCCGATCATCTGTTGCA
TATGCTATGAGGCAGTACTTTTTAAAAGTAAAAAATCAGATGATTCTTTTTGGGGAGGAGGATGTGCGAGTG
GCTAATTTGAAACCAAGAATCTCCTTTAATTTCTTTGTCACTGCACCTAAAAATGTGTCTGATATCATTCCT
AGAACTGAAGTTGAAAAGGCCATCAGGATGTCCCGGAGCCGTATCAATGATGCTTTCCGTCTGAATGACAAC
AGCCTAGAGTTTCTGGGGATACAGCCAACACTTGGACCTCCTAACCAGCCCCCTGTTTCCATATGGCTGATT
GTTTTTGGAGTTGTGATGGGAGTGATAGTGGTTGGCATTGTCATCCTGATCTTCACTGGGATCAGAGATCGG
AAGAAGAAAAATAAAGCAAGAAGTGGAGAAAATCCTTATGCCTCCATCGATATTAGCAAAGGAGAAAATAAT
CCAGGATTCCAAAACACTGATGATGTTCAGACCTCCTTT
13 changes: 13 additions & 0 deletions ACE2_HUMAN.fa
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>ACE2_HUMAN/1-805 Angiotensin-converting enzyme 2
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAF
LKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLL
EPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYD
YSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQK
PNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDN
ETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLF
HVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGA
KNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVA
YAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENN
PGFQNTDDVQTSF
29 changes: 29 additions & 0 deletions MutaBind2/2ajf-validation/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,K31D,0.97,yes,no,-0.0886,0.4269,0.0802,-0.0505,0.0883,0.0738,0.0123,-0.0018,0.4286
A,E37A,1.64,yes,yes,0.3423,0.0935,0.5293,0.3762,0.0123,-0.2625,0.1213,-0.0018,0.4286
A,D38A,0.71,yes,no,0.1708,-0.0402,-0.2347,0.1694,0.0593,-0.0072,0.1669,-0.0018,0.4286
A,Y41A,2.49,yes,yes,0.6543,0.3616,0.85,0.0082,0.5217,-0.4095,0.074,-0.0018,0.4286
A,K68D,0.29,no,no,-0.1121,-0.1339,-0.1603,0.4233,-0.3462,0.0767,0.1135,-0.0018,0.4286
A,E110P,-0.1,no,no,-0.1183,-0.0886,-0.3776,0.2616,-0.2185,-0.0314,0.0451,-0.0018,0.4286
A,E160R,0.04,no,no,-0.1506,-0.1202,-0.3637,0.5257,-0.3159,-0.0343,0.074,-0.0018,0.4286
A,R192D,1.35,no,no,-0.33,-0.1909,0.9201,0.3728,-0.1252,0.374,-0.1017,-0.0018,0.4286
A,R219D,0.38,no,no,-0.3611,-0.1943,0.9774,0.1281,-0.3851,-0.2371,0.0277,-0.0018,0.4286
A,H239Q,0.11,no,no,-0.055,-0.0528,-0.1253,-0.0268,0.0934,-0.145,-0.0045,-0.0018,0.4286
A,R273Q,-0.05,no,no,-0.0352,-0.0612,-0.1833,-0.0605,0.0074,-0.1546,0.0122,-0.0018,0.4286
A,K309D,0.67,no,no,-0.3696,-0.1856,0.8802,0.3729,-0.512,0.1278,-0.0698,-0.0018,0.4286
A,E312A,0.82,no,no,-0.1189,-0.1554,-0.1864,0.9692,0.2131,-0.2186,-0.1063,-0.0018,0.4286
A,T324A,0.2,yes,no,-0.0276,-0.1055,-0.4565,0.3782,-0.04,-0.0902,0.1121,-0.0018,0.4286
A,D350A,0.32,no,no,-0.1432,-0.1319,-0.3147,0.8466,-0.2545,-0.1289,0.0235,-0.0018,0.4286
A,D355A,1.21,yes,no,0.2077,0.1045,-0.2771,0.956,0.3695,-0.5034,-0.0707,-0.0018,0.4286
A,R357A,1.4,no,no,0.0121,0.5244,-0.2447,0.8952,0.1931,-0.3019,-0.1082,-0.0018,0.4286
A,M383A,0.69,no,no,-0.3796,-0.2729,0.8408,0.5278,-0.1899,-0.2385,-0.0275,-0.0018,0.4286
A,P389A,0.71,no,no,-0.3973,-0.2534,0.891,0.5928,-0.334,-0.2106,-0.0049,-0.0018,0.4286
A,R393A,0.88,no,no,-0.2913,-0.2507,0.9703,0.5503,-0.2927,-0.2141,-0.0176,-0.0018,0.4286
A,R559S,0.2,no,no,-0.159,-0.1177,-0.1572,0.2909,-0.2772,0.0862,0.1081,-0.0018,0.4286
A,F603T,0.15,no,no,-0.1057,-0.0686,-0.1382,0.1031,-0.1968,0.0582,0.0739,-0.0018,0.4286
A,K353H,2.03,yes,yes,0.1936,0.7992,-0.171,0.2448,0.2778,0.2285,0.0329,-0.0018,0.4286
A,K353A,2.41,yes,yes,0.5283,0.1549,0.9079,0.1994,-0.0448,0.193,0.0411,-0.0018,0.4286
A,K353D,2.56,yes,yes,0.5853,0.4487,1.1216,-0.1414,-0.0841,0.1739,0.0317,-0.0018,0.4286
A,L359K,-1.15,no,no,0.2162,0.2913,0.0366,-1.915,-0.2635,-0.0438,0.0968,-0.0018,0.4286
A,L359A,0.88,no,no,-0.0591,0.0122,1.2132,-0.5683,0.2435,-0.4408,0.0566,-0.0018,0.4286
29 changes: 29 additions & 0 deletions MutaBind2/6vw1-validation/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,K31D,1.7,yes,yes,-0.2995,0.6795,0.871,-0.2168,-0.1029,0.3676,-0.0301,-0.0018,0.4286
A,E37A,1.22,yes,no,-0.4197,0.139,0.87,0.4175,-0.1377,-0.1713,0.0961,-0.0018,0.4286
A,D38A,1.06,yes,no,0.14,0.673,-0.1516,0.0782,-0.155,0.0113,0.0422,-0.0018,0.4286
A,Y41A,2.78,yes,yes,0.4321,0.5651,0.8401,0.1511,0.6108,-0.3779,0.1331,-0.0018,0.4286
A,K68D,0.46,no,no,0.051,-0.1153,-0.1761,0.4639,-0.3395,0.0611,0.0852,-0.0018,0.4286
A,E110P,0.0,no,no,-0.1543,-0.1165,-0.1468,0.2377,-0.2677,-0.0275,0.0516,-0.0018,0.4286
A,E160R,0.1,no,no,-0.1744,-0.139,-0.1787,0.4552,-0.329,-0.0379,0.075,-0.0018,0.4286
A,R192D,1.32,no,no,-0.3331,-0.2029,0.9129,0.3728,-0.1439,0.3948,-0.1059,-0.0018,0.4286
A,R219D,0.37,no,no,-0.3436,-0.1815,0.9852,0.118,-0.4396,-0.201,0.0032,-0.0018,0.4286
A,H239Q,0.03,no,no,-0.0509,-0.0712,-0.1521,-0.008,0.019,-0.1258,-0.0027,-0.0018,0.4286
A,R273Q,0.04,no,no,-0.0683,-0.0633,-0.1229,-0.0055,-0.0217,-0.1068,0.0009,-0.0018,0.4286
A,K309D,0.47,no,no,-0.3668,-0.2194,0.7496,0.3782,-0.4464,-0.0918,0.0361,-0.0018,0.4286
A,E312A,0.7,no,no,-0.2348,-0.1311,-0.174,0.9445,0.2184,-0.2592,-0.0915,-0.0018,0.4286
A,T324A,0.36,yes,no,-0.1019,-0.1294,-0.1486,0.3608,-0.0962,-0.0692,0.1133,-0.0018,0.4286
A,D350A,0.56,no,no,-0.1232,-0.077,-0.7707,1.1521,-0.0274,-0.0382,0.0158,-0.0018,0.4286
A,D355A,1.19,yes,no,-0.0658,-0.0062,-0.2567,1.0258,0.4441,-0.3347,-0.0472,-0.0018,0.4286
A,R357A,1.3,no,no,-0.0564,0.1358,0.8116,0.5101,-0.011,-0.3834,-0.1367,-0.0018,0.4286
A,M383A,0.77,no,no,-0.4053,-0.2796,0.9913,0.5353,-0.1856,-0.2292,-0.0853,-0.0018,0.4286
A,P389A,0.75,no,no,-0.2669,-0.2015,0.4871,0.67,-0.2333,-0.117,-0.0137,-0.0018,0.4286
A,R393A,1.28,no,no,-0.1221,0.1187,0.9867,0.5519,-0.3681,-0.2802,-0.0367,-0.0018,0.4286
A,R559S,0.14,no,no,-0.1545,-0.1409,-0.1851,0.2892,-0.3141,0.107,0.1114,-0.0018,0.4286
A,F603T,0.11,no,no,-0.1032,-0.0826,-0.1578,0.0949,-0.1926,0.0638,0.0652,-0.0018,0.4286
A,K353H,1.96,yes,yes,-0.1359,0.5546,-0.0055,0.3895,0.4029,0.2977,0.0332,-0.0018,0.4286
A,K353A,1.95,yes,yes,-0.1012,0.8916,-0.3415,0.43,0.4397,0.2015,0.0008,-0.0018,0.4286
A,K353D,1.89,yes,yes,-0.1109,0.4619,0.8699,-0.0945,0.0421,0.2918,0.0073,-0.0018,0.4286
A,L359K,-0.89,no,no,0.095,0.2338,0.705,-2.1156,-0.0642,-0.227,0.0519,-0.0018,0.4286
A,L359A,0.78,no,no,-0.0419,0.0314,1.1529,-0.6052,0.232,-0.4553,0.039,-0.0018,0.4286
3 changes: 3 additions & 0 deletions MutaBind2/Bat/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutation ID,Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,dE_vdw_wt,bootstrapFC,Model_Bias
M1,A;A;A;A;A;A;A;A;A,Q24L;T27K;K31D;H34S;D38N;Y41H;M82N;Y83F;E329N,4.05,yes;yes;yes;yes;yes;yes;yes;yes;no,yes,0.9119,1.482,0.6522,-0.0231,-0.6695,0.3931,0.4561,-0.0099,0.8531
3 changes: 3 additions & 0 deletions MutaBind2/Civet/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutation ID,Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,dE_vdw_wt,bootstrapFC,Model_Bias
M1,A;A;A;A;A;A;A;A,Q24L;D30E;K31T;H34Y;E37Q;D38E;L45V;M82T,3.15,yes;yes;yes;yes;yes;yes;yes;yes,yes,-0.5048,1.1608,1.0012,0.5268,-0.721,0.4405,0.4049,-0.0099,0.8531
3 changes: 3 additions & 0 deletions MutaBind2/Mouse/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutation ID,Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,dE_vdw_wt,bootstrapFC,Model_Bias
M1,A;A;A;A;A;A;A;A;A,Q24N;D30N;K31N;H34Q;L79T;M82S;Y83F;E329A;K353H,4.53,yes;yes;yes;yes;yes;yes;yes;no;yes,yes,0.5492,1.4123,0.8795,0.166,-0.3493,0.6571,0.3695,-0.0099,0.8531
3 changes: 3 additions & 0 deletions MutaBind2/Pig/MutaBind2.csv
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This file was created by the MutaBind2 Server
Mutation ID,Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,dE_vdw_wt,bootstrapFC,Model_Bias
M1,A;A;A;A;A;A,Q24L;D30E;H34L;L79I;M82T;E329N,0.52,yes;yes;yes;yes;yes;yes,no,0.2981,0.1,-1.4476,0.7551,-0.2757,0.1567,0.0863,-0.0099,0.8531
3 changes: 3 additions & 0 deletions MutaBind2/R439N-model/MutaBind2.csv
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@@ -0,0 +1,3 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
E,R439N,-0.11,no,no,0.037,0.0101,0.0438,-0.859,0.0169,0.1561,0.0605,-0.0018,0.4286
42 changes: 42 additions & 0 deletions MutaBind2/R439N-model/alanine-scan/MutaBind2.csv
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@@ -0,0 +1,42 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,Q42A,1.13,yes,no,-0.0601,0.8872,-0.3411,0.4015,-0.1709,0.0219,-0.0382,-0.0018,0.4286
A,N330A,1.07,yes,no,0.0027,0.4449,-0.2884,0.5755,-0.0496,-0.0136,-0.0292,-0.0018,0.4286
A,R393A,1.37,no,no,-0.3068,0.4384,0.795,0.5375,-0.171,-0.3575,0.0077,-0.0018,0.4286
A,F390A,1.19,no,no,-0.3255,0.1205,0.9038,0.2367,0.0409,-0.2725,0.0547,-0.0018,0.4286
A,M82A,0.57,yes,no,-0.0491,0.0822,0.1327,0.1188,-0.2562,0.0672,0.049,-0.0018,0.4286
A,Y83A,2.54,yes,yes,0.1336,0.3317,0.9039,0.3408,0.6057,-0.2959,0.0947,-0.0018,0.4286
A,P84A,0.34,no,no,-0.1283,0.0226,0.0215,0.3351,-0.3183,-0.0591,0.0364,-0.0018,0.4286
A,Q24A,1.4,yes,no,0.3133,0.2219,-0.3018,0.4444,0.1605,0.0475,0.0843,-0.0018,0.4286
A,K26A,0.42,no,no,-0.1385,0.166,-0.2174,0.469,-0.3427,0.0058,0.0559,-0.0018,0.4286
A,T27A,0.9,yes,no,0.1758,0.1002,-0.3022,-0.03,0.2546,0.1926,0.0794,-0.0018,0.4286
A,T20A,0.19,no,no,-0.1086,0.1413,-0.3603,0.325,-0.2599,-0.0072,0.0345,-0.0018,0.4286
A,I21A,0.44,no,no,-0.3156,0.0583,0.8642,-0.0328,-0.3968,-0.2203,0.0575,-0.0018,0.4286
A,E23A,0.39,yes,no,-0.0393,0.0747,-0.1681,0.3603,-0.3115,-0.0321,0.0805,-0.0018,0.4286
A,L45A,1.07,yes,no,-0.0209,0.1321,0.0648,0.3009,0.1506,-0.0649,0.0852,-0.0018,0.4286
A,F28A,2.16,yes,yes,-0.2506,0.1191,0.8499,0.4905,0.526,-0.1733,0.1712,-0.0018,0.4286
A,L29A,1.19,no,no,-0.3387,0.1697,0.8865,0.4422,0.3083,-0.7647,0.0579,-0.0018,0.4286
A,Y41A,2.59,yes,yes,-0.0671,0.4576,0.9843,0.2872,0.6586,-0.3159,0.1552,-0.0018,0.4286
A,F356A,1.22,no,no,-0.3869,0.1449,0.9108,0.6538,0.0047,-0.5262,-0.0111,-0.0018,0.4286
A,G326A,-0.14,yes,no,-0.2206,0.0224,-0.3628,0.0546,0.0926,-0.1542,0.0049,-0.0018,0.4286
A,T324A,0.6,yes,no,-0.1261,0.129,-0.1555,0.3169,-0.0039,-0.0537,0.07,-0.0018,0.4286
A,Q325A,0.39,yes,no,-0.1729,0.0905,-0.2237,0.4882,-0.3571,0.0906,0.0519,-0.0018,0.4286
A,E329A,0.28,no,no,-0.1946,0.0316,-0.2427,0.5005,-0.3464,0.0588,0.05,-0.0018,0.4286
A,Q76A,-0.08,no,no,0.0537,0.0649,-0.26,-0.1763,0.06,-0.2127,-0.0406,-0.0018,0.4286
A,L79A,0.6,yes,no,-0.0646,-0.0058,0.158,-0.0081,0.0397,0.0278,0.0297,-0.0018,0.4286
A,L39A,1.46,no,no,-0.0941,0.3245,0.8495,0.2606,0.0462,-0.3572,0.0072,-0.0018,0.4286
A,D38A,1.33,yes,no,-0.1372,0.8062,-0.093,0.0818,0.246,-0.0813,0.0822,-0.0018,0.4286
A,N33A,0.92,no,no,-0.0571,0.0358,-0.291,0.9924,0.2935,-0.3876,-0.0904,-0.0018,0.4286
A,F32A,1.45,no,no,-0.3113,0.1253,0.8171,0.4741,0.5474,-0.7522,0.1267,-0.0018,0.4286
A,K31A,1.34,yes,no,-0.038,0.6138,-0.3506,0.3948,0.1509,0.1892,-0.051,-0.0018,0.4286
A,D30A,0.3,yes,no,-0.0912,0.0539,-0.3621,0.3858,-0.1581,-0.0247,0.0662,-0.0018,0.4286
A,E37A,1.44,yes,no,-0.4046,0.3551,0.8519,0.3962,0.0233,-0.3225,0.1172,-0.0018,0.4286
A,E35A,1.03,yes,no,-0.0468,0.7599,-0.3082,0.4872,-0.1475,-0.1126,-0.0259,-0.0018,0.4286
A,H34A,0.76,yes,no,0.2213,0.0707,-0.3053,-0.0075,0.1743,0.1078,0.0754,-0.0018,0.4286
A,R357A,1.49,no,no,-0.0862,0.3915,0.8459,0.4959,-0.0888,-0.415,-0.0848,-0.0018,0.4286
A,S19A,0.36,yes,no,-0.1309,0.2272,-0.2152,0.2074,-0.2947,0.1083,0.0279,-0.0018,0.4286
A,D355A,1.81,yes,yes,-0.008,0.0519,0.7878,0.4797,0.5204,-0.5038,0.0514,-0.0018,0.4286
A,G354A,1.29,yes,no,-0.3907,0.1017,0.9413,0.1802,0.111,-0.2024,0.1208,-0.0018,0.4286
A,K353A,3.01,yes,yes,-0.0332,0.4311,1.1543,0.2535,0.4856,0.3031,-0.0064,-0.0018,0.4286
A,G352A,1.68,no,yes,-0.2651,0.1897,0.8124,0.452,0.5866,-0.7205,0.1985,-0.0018,0.4286
A,L351A,1.52,no,yes,-0.3446,0.1868,0.8086,0.4283,0.567,-0.7483,0.1924,-0.0018,0.4286
4 changes: 4 additions & 0 deletions MutaBind2/R439N-model/gnomAD-extended-interface/MutaBind2.csv
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@@ -0,0 +1,4 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,G326E,-0.59,yes,no,-0.3665,0.5874,-0.1284,-0.7526,-0.2091,-0.2037,0.0579,-0.0018,0.4286
A,G352V,1.69,no,yes,0.0962,0.1547,0.9143,0.3443,0.5331,-0.9021,0.1204,-0.0018,0.4286
9 changes: 9 additions & 0 deletions MutaBind2/R439N-model/gnomAD-interface/MutaBind2.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,S19P,0.24,yes,no,-0.188,0.1057,-0.1676,0.1994,-0.2985,0.0901,0.0735,-0.0018,0.4286
A,T27A,0.88,yes,no,0.1773,0.077,-0.2959,-0.0336,0.255,0.1943,0.0814,-0.0018,0.4286
A,E35K,1.02,yes,no,-0.2343,0.8831,-0.2408,0.4477,-0.1872,-0.0683,-0.0054,-0.0018,0.4286
A,E37K,1.93,yes,yes,-0.0167,0.7611,0.915,0.2799,-0.044,-0.4528,0.0608,-0.0018,0.4286
A,M82I,0.18,yes,no,-0.1161,0.0991,-0.1634,0.1759,-0.2772,-0.0106,0.0452,-0.0018,0.4286
A,E329G,0.26,no,no,-0.203,0.0143,-0.1845,0.4622,-0.366,0.0523,0.0556,-0.0018,0.4286
A,D355N,1.7,yes,yes,-0.1997,0.0112,0.7802,0.4101,0.5488,-0.4023,0.1233,-0.0018,0.4286
6 changes: 6 additions & 0 deletions MutaBind2/R439N-model/ortholog-single-submission/MutaBind2.csv
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@@ -0,0 +1,6 @@
This file was created by the MutaBind2 Server
Mutation ID,Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,dE_vdw_wt,bootstrapFC,Model_Bias
M1,A;A;A;A;A;A;A;A;A,Q24L;T27K;K31D;H34S;D38N;Y41H;M82N;Y83F;E329N,2.99,yes;yes;yes;yes;yes;yes;yes;yes;no,yes,-0.2421,1.2061,0.9846,0.0628,-0.6928,0.5153,0.3127,-0.0099,0.8531
M2,A;A;A;A;A;A;A;A,Q24L;D30E;K31T;H34Y;E37Q;D38E;L45V;M82T,2.72,yes;yes;yes;yes;yes;yes;yes;yes,yes,-0.5966,1.0142,0.9319,0.5169,-0.7707,0.4128,0.3644,-0.0099,0.8531
M3,A;A;A;A;A;A;A;A;A,Q24N;D30N;K31N;H34Q;L79T;M82S;Y83F;E329A;K353H,3.28,yes;yes;yes;yes;yes;yes;yes;no;yes,yes,-0.6099,1.1869,0.943,0.4523,-0.7034,0.8163,0.3517,-0.0099,0.8531
M4,A;A;A;A;A;A,Q24L;D30E;H34L;L79I;M82T;E329N,1.45,yes;yes;yes;yes;yes;no,no,-0.1239,-0.0372,0.5969,0.4539,-0.7055,0.1818,0.2362,-0.0099,0.8531
30 changes: 30 additions & 0 deletions MutaBind2/alanine-scan/MutaBind2.csv
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@@ -0,0 +1,30 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,Q42A,0.72,yes,no,0.2296,0.0134,-0.279,0.5161,-0.2715,-0.0155,0.1029,-0.0018,0.4286
A,N330A,0.96,yes,no,0.2084,0.0895,-0.2991,0.7036,-0.1015,-0.0774,0.0068,-0.0018,0.4286
A,R393A,1.28,no,no,-0.1221,0.1298,0.9756,0.5503,-0.3676,-0.2806,-0.0348,-0.0018,0.4286
A,M82A,0.41,yes,no,-0.1022,-0.1049,0.109,0.1787,-0.2642,0.0859,0.0832,-0.0018,0.4286
A,Y83A,2.17,yes,yes,0.304,-0.1037,1.0137,0.4546,0.3227,-0.235,-0.0136,-0.0018,0.4286
A,Q24A,0.94,yes,no,0.2922,-0.0402,-0.3857,0.4792,0.0407,0.0249,0.0982,-0.0018,0.4286
A,T27A,0.63,yes,no,-0.0414,-0.0965,-0.1375,0.0313,0.2647,0.1447,0.035,-0.0018,0.4286
A,L45A,0.76,yes,no,0.0755,-0.0854,0.2397,0.2131,-0.0306,-0.1112,0.0363,-0.0018,0.4286
A,F28A,1.0,yes,no,-0.3352,-0.3259,0.893,0.5771,0.1422,-0.2688,-0.1102,-0.0018,0.4286
A,L29A,0.69,no,no,-0.3723,-0.2615,0.9533,0.5124,0.009,-0.4857,-0.0899,-0.0018,0.4286
A,Y41A,2.77,yes,yes,0.429,0.5573,0.8401,0.1511,0.6108,-0.3779,0.1331,-0.0018,0.4286
A,G326A,-0.35,yes,no,-0.2131,-0.1138,-0.38,0.045,0.0685,-0.1384,-0.0453,-0.0018,0.4286
A,Q325A,0.27,yes,no,-0.0157,-0.1468,-0.1968,0.4543,-0.3452,0.0283,0.067,-0.0018,0.4286
A,E329A,0.21,no,no,-0.1398,-0.0674,-0.2508,0.4669,-0.3539,0.0754,0.0526,-0.0018,0.4286
A,L79A,0.47,yes,no,-0.0217,-0.072,-0.0326,0.0819,0.0382,0.0196,0.0301,-0.0018,0.4286
A,D38A,1.05,yes,no,0.1429,0.6604,-0.15,0.0728,-0.1546,0.012,0.0421,-0.0018,0.4286
A,S19A,0.12,yes,no,-0.0969,-0.0707,-0.1563,0.2368,-0.2683,-0.0239,0.0738,-0.0018,0.4286
A,K31A,1.07,yes,no,-0.1535,0.1711,-0.1905,0.4705,0.1743,0.1584,0.0155,-0.0018,0.4286
A,D30A,0.18,yes,no,-0.0253,-0.1112,-0.3303,0.4042,-0.2623,0.0154,0.0635,-0.0018,0.4286
A,E37A,1.21,yes,no,-0.4255,0.1223,0.8766,0.4132,-0.1319,-0.1686,0.0988,-0.0018,0.4286
A,E35A,0.96,yes,no,-0.2574,0.9483,-0.3057,0.5195,-0.3129,-0.0203,-0.0334,-0.0018,0.4286
A,H34A,0.33,yes,no,0.1909,0.0409,-0.3113,0.1117,-0.2827,0.047,0.1098,-0.0018,0.4286
A,R357A,1.31,no,no,-0.0549,0.1452,0.816,0.5118,-0.0139,-0.3859,-0.1373,-0.0018,0.4286
A,F356A,0.68,no,no,-0.4246,-0.2889,0.9304,0.6291,-0.0553,-0.3701,-0.1658,-0.0018,0.4286
A,D355A,1.2,yes,no,-0.0657,-0.0107,-0.2544,1.0262,0.4537,-0.3284,-0.0485,-0.0018,0.4286
A,G354A,0.58,yes,no,-0.3762,-0.2664,0.9346,0.1441,-0.0598,-0.1806,-0.0378,-0.0018,0.4286
A,K353A,1.97,yes,yes,-0.1,0.9144,-0.3417,0.4276,0.4381,0.201,0.0026,-0.0018,0.4286
A,G352A,0.47,no,no,-0.2686,-0.22,0.9093,0.2864,-0.0186,-0.5502,-0.1,-0.0018,0.4286
9 changes: 9 additions & 0 deletions MutaBind2/gnomAD-interface/MutaBind2.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
This file was created by the MutaBind2 Server
Mutated Chain,Mutation,DDG,Interface?,Deleterious?,DDE_vdw,DDG_solv,DDG_fold,CS,SA_com_wt,SA_part_wt,N_cont_wt,bootstrapFC,Model_Bias
A,S19P,0.08,yes,no,-0.1241,-0.1197,-0.1586,0.2505,-0.2804,0.0103,0.0757,-0.0018,0.4286
A,T27A,0.64,yes,no,-0.0347,-0.0829,-0.139,0.0341,0.2648,0.1305,0.0359,-0.0018,0.4286
A,E35K,0.38,yes,no,-0.2286,0.0473,-0.136,0.3559,-0.1565,-0.0098,0.0791,-0.0018,0.4286
A,E37K,0.96,yes,no,-0.1633,0.7271,0.0088,0.2456,0.0008,-0.2978,0.0113,-0.0018,0.4286
A,M82I,0.23,yes,no,-0.1547,-0.1048,0.0426,0.1563,-0.2867,0.072,0.0774,-0.0018,0.4286
A,E329G,0.45,no,no,-0.0517,-0.0192,-0.1568,0.44,-0.3483,0.0979,0.0656,-0.0018,0.4286
A,D355N,1.01,yes,no,-0.0809,-0.1315,-0.2503,0.9693,0.4908,-0.336,-0.0818,-0.0018,0.4286
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