├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.md │ └── feature_request.md ├── dependabot.yml └── workflows │ ├── build_test.yml │ ├── cffconvert.yml │ └── publish_pypi.yml ├── .gitignore ├── .zenodo.json ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin ├── iScore.graph ├── iScore.graph.mpi ├── iScore.h5x ├── iScore.kernel ├── iScore.kernel.mpi ├── iScore.predict ├── iScore.predict.mpi ├── iScore.svm ├── iScore.train └── iScore.train.mpi ├── docs ├── Makefile ├── comp.png ├── conf.py ├── conf_save.py ├── doc.rst ├── gpu.rst ├── graph.rst ├── h5x_iscore.png ├── index.rst ├── install.rst ├── intro.rst ├── make.bat ├── pssm.rst ├── quick.rst ├── svm.rst ├── viz.rst └── workflow.rst ├── example ├── graph │ ├── 1ATN.mat │ ├── 1ATN.pkl │ ├── create_graph.py │ └── input │ │ ├── 1ATN.A.pdb.pssm │ │ ├── 1ATN.B.pdb.pssm │ │ ├── 1ATN.pckl │ │ └── 1ATN.pdb ├── h5x │ └── graphs.hdf5 ├── kernel │ ├── check │ │ ├── graphMAT │ │ │ ├── 1IRA.mat │ │ │ └── 2OZA.mat │ │ └── kernelMAT │ │ │ └── K.mat │ ├── create_kernel.py │ ├── kernel.pkl │ ├── pdb │ │ ├── 1IRA.pdb │ │ └── 2OZA.pdb │ ├── pssm │ │ ├── 1IRA.A.pdb.pssm │ │ ├── 1IRA.B.pdb.pssm │ │ ├── 2OZA.A.pdb.pssm │ │ └── 2OZA.B.pdb.pssm │ ├── testID.lst │ └── trainID.lst ├── test │ ├── pdb │ │ ├── 1ACB_1w.pdb │ │ ├── 1ACB_2w.pdb │ │ ├── 1ACB_3w.pdb │ │ ├── 1ACB_4w.pdb │ │ └── 1ACB_5w.pdb │ └── pssm │ │ ├── 1ACB_1w.A.pdb.pssm │ │ ├── 1ACB_1w.B.pdb.pssm │ │ ├── 1ACB_2w.A.pdb.pssm │ │ ├── 1ACB_2w.B.pdb.pssm │ │ ├── 1ACB_3w.A.pdb.pssm │ │ ├── 1ACB_3w.B.pdb.pssm │ │ ├── 1ACB_4w.A.pdb.pssm │ │ ├── 1ACB_4w.B.pdb.pssm │ │ ├── 1ACB_5w.A.pdb.pssm │ │ └── 1ACB_5w.B.pdb.pssm ├── train │ ├── caseID.lst │ ├── pdb │ │ ├── 7CEI_400w.pdb │ │ ├── 7CEI_40w.pdb │ │ ├── 7CEI_41w.pdb │ │ ├── 7CEI_42w.pdb │ │ ├── 7CEI_43w.pdb │ │ ├── 7CEI_44w.pdb │ │ ├── 7CEI_45w.pdb │ │ ├── 7CEI_46w.pdb │ │ ├── 7CEI_47w.pdb │ │ ├── 7CEI_48w.pdb │ │ ├── 7CEI_49w.pdb │ │ └── 7CEI_4w.pdb │ └── pssm │ │ ├── 7CEI_400w.A.pdb.pssm │ │ ├── 7CEI_400w.B.pdb.pssm │ │ ├── 7CEI_40w.A.pdb.pssm │ │ ├── 7CEI_40w.B.pdb.pssm │ │ ├── 7CEI_41w.A.pdb.pssm │ │ ├── 7CEI_41w.B.pdb.pssm │ │ ├── 7CEI_42w.A.pdb.pssm │ │ ├── 7CEI_42w.B.pdb.pssm │ │ ├── 7CEI_43w.A.pdb.pssm │ │ ├── 7CEI_43w.B.pdb.pssm │ │ ├── 7CEI_44w.A.pdb.pssm │ │ ├── 7CEI_44w.B.pdb.pssm │ │ ├── 7CEI_45w.A.pdb.pssm │ │ ├── 7CEI_45w.B.pdb.pssm │ │ ├── 7CEI_46w.A.pdb.pssm │ │ ├── 7CEI_46w.B.pdb.pssm │ │ ├── 7CEI_47w.A.pdb.pssm │ │ ├── 7CEI_47w.B.pdb.pssm │ │ ├── 7CEI_48w.A.pdb.pssm │ │ ├── 7CEI_48w.B.pdb.pssm │ │ ├── 7CEI_49w.A.pdb.pssm │ │ ├── 7CEI_49w.B.pdb.pssm │ │ ├── 7CEI_4w.A.pdb.pssm │ │ └── 7CEI_4w.B.pdb.pssm └── training_dataset │ ├── README.md │ ├── caseID.lst │ ├── pdb │ ├── 1ACB.pdb │ ├── 1ACB_235w.pdb │ ├── 1AK4.pdb │ ├── 1ATN.pdb │ ├── 1AVX.pdb │ ├── 1AY7.pdb │ ├── 1AY7_106w.pdb │ ├── 1AY7_274w.pdb │ ├── 1AY7_288w.pdb │ ├── 1B6C.pdb │ ├── 1B6C_196w.pdb │ ├── 1B6C_272w.pdb │ ├── 1B6C_310w.pdb │ ├── 1BKD.pdb │ ├── 1BUH.pdb │ ├── 1BUH_110w.pdb │ ├── 1BUH_89w.pdb │ ├── 1BVN.pdb │ ├── 1BVN_141w.pdb │ ├── 1BVN_175w.pdb │ ├── 1BVN_237w.pdb │ ├── 1BVN_289w.pdb │ ├── 1BVN_40w.pdb │ ├── 1CGI.pdb │ ├── 1CGI_243w.pdb │ ├── 1CLV.pdb │ ├── 1D6R.pdb │ ├── 1D6R_127w.pdb │ ├── 1D6R_217w.pdb │ ├── 1DFJ.pdb │ ├── 1DFJ_95w.pdb │ ├── 1E6E.pdb │ ├── 1E6E_119w.pdb │ ├── 1E6E_201w.pdb │ ├── 1E96.pdb │ ├── 1E96_383w.pdb │ ├── 1EAW.pdb │ ├── 1EFN.pdb │ ├── 1EFN_205w.pdb │ ├── 1EFN_391w.pdb │ ├── 1EWY.pdb │ ├── 1EWY_23w.pdb │ ├── 1F34.pdb │ ├── 1F34_296w.pdb │ ├── 1F34_70w.pdb │ ├── 1F6M.pdb │ ├── 1FC2.pdb │ ├── 1FC2_177w.pdb │ ├── 1FC2_307w.pdb │ ├── 1FC2_41w.pdb │ ├── 1FFW.pdb │ ├── 1FFW_160w.pdb │ ├── 1FFW_190w.pdb │ ├── 1FFW_342w.pdb │ ├── 1FLE.pdb │ ├── 1FQ1.pdb │ ├── 1FQJ.pdb │ ├── 1GCQ.pdb │ ├── 1GHQ.pdb │ ├── 1GL1.pdb │ ├── 1GL1_145w.pdb │ ├── 1GLA.pdb │ ├── 1GLA_400w.pdb │ ├── 1GPW.pdb │ ├── 1GPW_142w.pdb │ ├── 1GPW_271w.pdb │ ├── 1GPW_99w.pdb │ ├── 1GRN.pdb │ ├── 1GRN_110w.pdb │ ├── 1GRN_148w.pdb │ ├── 1GRN_21w.pdb │ ├── 1GXD.pdb │ ├── 1H1V.pdb │ ├── 1H9D.pdb │ ├── 1H9D_143w.pdb │ ├── 1HE1.pdb │ ├── 1HE8.pdb │ ├── 1I2M.pdb │ ├── 1I2M_111w.pdb │ ├── 1I2M_138w.pdb │ ├── 1IBR.pdb │ ├── 1IRA.pdb │ ├── 1J2J.pdb │ ├── 1J2J_282w.pdb │ ├── 1JIW.pdb │ ├── 1JK9.pdb │ ├── 1JTG.pdb │ ├── 1JTG_259w.pdb │ ├── 1JTG_315w.pdb │ ├── 1JTG_358w.pdb │ ├── 1KAC.pdb │ ├── 1KAC_317w.pdb │ ├── 1KTZ.pdb │ ├── 1KXP.pdb │ ├── 1KXQ.pdb │ ├── 1LFD.pdb │ ├── 1LFD_202w.pdb │ ├── 1LFD_272w.pdb │ ├── 1LFD_292w.pdb │ ├── 1LFD_359w.pdb │ ├── 1LFD_368w.pdb │ ├── 1M10.pdb │ ├── 1MAH.pdb │ ├── 1MAH_241w.pdb │ ├── 1MQ8.pdb │ ├── 1NW9.pdb │ ├── 1NW9_12w.pdb │ ├── 1NW9_70w.pdb │ ├── 1OC0.pdb │ ├── 1OC0_281w.pdb │ ├── 1OPH.pdb │ ├── 1OYV.pdb │ ├── 1OYV_77w.pdb │ ├── 1PPE.pdb │ ├── 1PVH.pdb │ ├── 1PVH_151w.pdb │ ├── 1PVH_394w.pdb │ ├── 1PXV.pdb │ ├── 1QA9.pdb │ ├── 1R0R.pdb │ ├── 1R0R_282w.pdb │ ├── 1R6Q.pdb │ ├── 1R6Q_170w.pdb │ ├── 1R8S.pdb │ ├── 1S1Q.pdb │ ├── 1S1Q_336w.pdb │ ├── 1S1Q_77w.pdb │ ├── 1SBB.pdb │ ├── 1SYX.pdb │ ├── 1T6B.pdb │ ├── 1TMQ.pdb │ ├── 1TMQ_10w.pdb │ ├── 1US7.pdb │ ├── 1US7_301w.pdb │ ├── 1WQ1.pdb │ ├── 1WQ1_348w.pdb │ ├── 1XD3.pdb │ ├── 1XQS.pdb │ ├── 1XQS_217w.pdb │ ├── 1XQS_32w.pdb │ ├── 1Y64.pdb │ ├── 1YVB.pdb │ ├── 1YVB_104w.pdb │ ├── 1YVB_105w.pdb │ ├── 1YVB_349w.pdb │ ├── 1Z0K.pdb │ ├── 1Z0K_324w.pdb │ ├── 1Z0K_93w.pdb │ ├── 1Z5Y.pdb │ ├── 1Z5Y_203w.pdb │ ├── 1Z5Y_261w.pdb │ ├── 1ZHH.pdb │ ├── 1ZHH_319w.pdb │ ├── 1ZHH_364w.pdb │ ├── 1ZHI.pdb │ ├── 1ZHI_114w.pdb │ ├── 1ZHI_295w.pdb │ ├── 1ZHI_316w.pdb │ ├── 1ZLI.pdb │ ├── 1ZM4.pdb │ ├── 2A5T.pdb │ ├── 2A5T_145w.pdb │ ├── 2A9K.pdb │ ├── 2A9K_214w.pdb │ ├── 2A9K_346w.pdb │ ├── 2ABZ.pdb │ ├── 2ABZ_330w.pdb │ ├── 2AJF.pdb │ ├── 2AYO.pdb │ ├── 2AYO_215w.pdb │ ├── 2B42.pdb │ ├── 2BTF.pdb │ ├── 2BTF_133w.pdb │ ├── 2BTF_33w.pdb │ ├── 2BTF_383w.pdb │ ├── 2C0L.pdb │ ├── 2CFH.pdb │ ├── 2FJU.pdb │ ├── 2FJU_194w.pdb │ ├── 2G77.pdb │ ├── 2H7V.pdb │ ├── 2HLE.pdb │ ├── 2HLE_185w.pdb │ ├── 2HLE_39w.pdb │ ├── 2HLE_400w.pdb │ ├── 2HQS.pdb │ ├── 2HQS_331w.pdb │ ├── 2HRK.pdb │ ├── 2I25.pdb │ ├── 2I9B.pdb │ ├── 2IDO.pdb │ ├── 2J0T.pdb │ ├── 2J7P.pdb │ ├── 2J7P_255w.pdb │ ├── 2J7P_331w.pdb │ ├── 2NZ8.pdb │ ├── 2O3B.pdb │ ├── 2O3B_137w.pdb │ ├── 2O3B_366w.pdb │ ├── 2O3B_386w.pdb │ ├── 2O8V.pdb │ ├── 2OOB.pdb │ ├── 2OOB_76w.pdb │ ├── 2OT3.pdb │ ├── 2OUL.pdb │ ├── 2OUL_242w.pdb │ ├── 2OZA.pdb │ ├── 2PCC.pdb │ ├── 2PCC_166w.pdb │ ├── 2PCC_182w.pdb │ ├── 2PCC_257w.pdb │ ├── 2SIC.pdb │ ├── 2SIC_168w.pdb │ ├── 2SIC_41w.pdb │ ├── 2SIC_88w.pdb │ ├── 2SNI.pdb │ ├── 2VDB.pdb │ ├── 2Z0E.pdb │ ├── 3CPH.pdb │ ├── 3CPH_262w.pdb │ ├── 3D5S.pdb │ ├── 3D5S_188w.pdb │ ├── 3D5S_258w.pdb │ ├── 3D5S_82w.pdb │ ├── 3SGQ.pdb │ ├── 3SGQ_274w.pdb │ ├── 4CPA.pdb │ ├── 7CEI.pdb │ ├── 7CEI_127w.pdb │ ├── 7CEI_169w.pdb │ ├── 7CEI_321w.pdb │ ├── 7CEI_331w.pdb │ ├── 7CEI_55w.pdb │ └── BOYV.pdb │ └── pssm │ ├── 1ACB.A.pdb.pssm │ ├── 1ACB.B.pdb.pssm │ ├── 1ACB_235w.A.pdb.pssm │ ├── 1ACB_235w.B.pdb.pssm │ ├── 1AK4.A.pdb.pssm │ ├── 1AK4.B.pdb.pssm │ ├── 1ATN.A.pdb.pssm │ ├── 1ATN.B.pdb.pssm │ ├── 1AVX.A.pdb.pssm │ ├── 1AVX.B.pdb.pssm │ ├── 1AY7.A.pdb.pssm │ ├── 1AY7.B.pdb.pssm │ ├── 1AY7_106w.A.pdb.pssm │ ├── 1AY7_106w.B.pdb.pssm │ ├── 1AY7_274w.A.pdb.pssm │ ├── 1AY7_274w.B.pdb.pssm │ ├── 1AY7_288w.A.pdb.pssm │ ├── 1AY7_288w.B.pdb.pssm │ ├── 1B6C.A.pdb.pssm │ ├── 1B6C.B.pdb.pssm │ ├── 1B6C_196w.A.pdb.pssm │ ├── 1B6C_196w.B.pdb.pssm │ ├── 1B6C_272w.A.pdb.pssm │ ├── 1B6C_272w.B.pdb.pssm │ ├── 1B6C_310w.A.pdb.pssm │ ├── 1B6C_310w.B.pdb.pssm │ ├── 1BKD.A.pdb.pssm │ ├── 1BKD.B.pdb.pssm │ ├── 1BUH.A.pdb.pssm │ ├── 1BUH.B.pdb.pssm │ ├── 1BUH_110w.A.pdb.pssm │ ├── 1BUH_110w.B.pdb.pssm │ ├── 1BUH_89w.A.pdb.pssm │ ├── 1BUH_89w.B.pdb.pssm │ ├── 1BVN.A.pdb.pssm │ ├── 1BVN.B.pdb.pssm │ ├── 1BVN_141w.A.pdb.pssm │ ├── 1BVN_141w.B.pdb.pssm │ ├── 1BVN_175w.A.pdb.pssm │ ├── 1BVN_175w.B.pdb.pssm │ ├── 1BVN_237w.A.pdb.pssm │ ├── 1BVN_237w.B.pdb.pssm │ ├── 1BVN_289w.A.pdb.pssm │ ├── 1BVN_289w.B.pdb.pssm │ ├── 1BVN_40w.A.pdb.pssm │ ├── 1BVN_40w.B.pdb.pssm │ ├── 1CGI.A.pdb.pssm │ ├── 1CGI.B.pdb.pssm │ ├── 1CGI_243w.A.pdb.pssm │ ├── 1CGI_243w.B.pdb.pssm │ ├── 1CLV.A.pdb.pssm │ ├── 1CLV.B.pdb.pssm │ ├── 1D6R.A.pdb.pssm │ ├── 1D6R.B.pdb.pssm │ ├── 1D6R_127w.A.pdb.pssm │ ├── 1D6R_127w.B.pdb.pssm │ ├── 1D6R_217w.A.pdb.pssm │ ├── 1D6R_217w.B.pdb.pssm │ ├── 1DFJ.A.pdb.pssm │ ├── 1DFJ.B.pdb.pssm │ ├── 1DFJ_95w.A.pdb.pssm │ ├── 1DFJ_95w.B.pdb.pssm │ ├── 1E6E.A.pdb.pssm │ ├── 1E6E.B.pdb.pssm │ ├── 1E6E_119w.A.pdb.pssm │ ├── 1E6E_119w.B.pdb.pssm │ ├── 1E6E_201w.A.pdb.pssm │ ├── 1E6E_201w.B.pdb.pssm │ ├── 1E96.A.pdb.pssm │ ├── 1E96.B.pdb.pssm │ ├── 1E96_383w.A.pdb.pssm │ ├── 1E96_383w.B.pdb.pssm │ ├── 1EAW.A.pdb.pssm │ ├── 1EAW.B.pdb.pssm │ ├── 1EFN.A.pdb.pssm │ ├── 1EFN.B.pdb.pssm │ ├── 1EFN_205w.A.pdb.pssm │ ├── 1EFN_205w.B.pdb.pssm │ ├── 1EFN_391w.A.pdb.pssm │ ├── 1EFN_391w.B.pdb.pssm │ ├── 1EWY.A.pdb.pssm │ ├── 1EWY.B.pdb.pssm │ ├── 1EWY_23w.A.pdb.pssm │ ├── 1EWY_23w.B.pdb.pssm │ ├── 1F34.A.pdb.pssm │ ├── 1F34.B.pdb.pssm │ ├── 1F34_296w.A.pdb.pssm │ ├── 1F34_296w.B.pdb.pssm │ ├── 1F34_70w.A.pdb.pssm │ ├── 1F34_70w.B.pdb.pssm │ ├── 1F6M.A.pdb.pssm │ ├── 1F6M.B.pdb.pssm │ ├── 1FC2.A.pdb.pssm │ ├── 1FC2.B.pdb.pssm │ ├── 1FC2_177w.A.pdb.pssm │ ├── 1FC2_177w.B.pdb.pssm │ ├── 1FC2_307w.A.pdb.pssm │ ├── 1FC2_307w.B.pdb.pssm │ ├── 1FC2_41w.A.pdb.pssm │ ├── 1FC2_41w.B.pdb.pssm │ ├── 1FFW.A.pdb.pssm │ ├── 1FFW.B.pdb.pssm │ ├── 1FFW_160w.A.pdb.pssm │ ├── 1FFW_160w.B.pdb.pssm │ ├── 1FFW_190w.A.pdb.pssm │ ├── 1FFW_190w.B.pdb.pssm │ ├── 1FFW_342w.A.pdb.pssm │ ├── 1FFW_342w.B.pdb.pssm │ ├── 1FLE.A.pdb.pssm │ ├── 1FLE.B.pdb.pssm │ ├── 1FQ1.A.pdb.pssm │ ├── 1FQ1.B.pdb.pssm │ ├── 1FQJ.A.pdb.pssm │ ├── 1FQJ.B.pdb.pssm │ ├── 1GCQ.A.pdb.pssm │ ├── 1GCQ.B.pdb.pssm │ ├── 1GHQ.A.pdb.pssm │ ├── 1GHQ.B.pdb.pssm │ ├── 1GL1.A.pdb.pssm │ ├── 1GL1.B.pdb.pssm │ ├── 1GL1_145w.A.pdb.pssm │ ├── 1GL1_145w.B.pdb.pssm │ ├── 1GLA.A.pdb.pssm │ ├── 1GLA.B.pdb.pssm │ ├── 1GLA_400w.A.pdb.pssm │ ├── 1GLA_400w.B.pdb.pssm │ ├── 1GPW.A.pdb.pssm │ ├── 1GPW.B.pdb.pssm │ ├── 1GPW_142w.A.pdb.pssm │ ├── 1GPW_142w.B.pdb.pssm │ ├── 1GPW_271w.A.pdb.pssm │ ├── 1GPW_271w.B.pdb.pssm │ ├── 1GPW_99w.A.pdb.pssm │ ├── 1GPW_99w.B.pdb.pssm │ ├── 1GRN.A.pdb.pssm │ ├── 1GRN.B.pdb.pssm │ ├── 1GRN_110w.A.pdb.pssm │ ├── 1GRN_110w.B.pdb.pssm │ ├── 1GRN_148w.A.pdb.pssm │ ├── 1GRN_148w.B.pdb.pssm │ ├── 1GRN_21w.A.pdb.pssm │ ├── 1GRN_21w.B.pdb.pssm │ ├── 1GXD.A.pdb.pssm │ ├── 1GXD.B.pdb.pssm │ ├── 1H1V.A.pdb.pssm │ ├── 1H1V.B.pdb.pssm │ ├── 1H9D.A.pdb.pssm │ ├── 1H9D.B.pdb.pssm │ ├── 1H9D_143w.A.pdb.pssm │ ├── 1H9D_143w.B.pdb.pssm │ ├── 1HE1.A.pdb.pssm │ ├── 1HE1.B.pdb.pssm │ ├── 1HE8.A.pdb.pssm │ ├── 1HE8.B.pdb.pssm │ ├── 1I2M.A.pdb.pssm │ ├── 1I2M.B.pdb.pssm │ ├── 1I2M_111w.A.pdb.pssm │ ├── 1I2M_111w.B.pdb.pssm │ ├── 1I2M_138w.A.pdb.pssm │ ├── 1I2M_138w.B.pdb.pssm │ ├── 1IBR.A.pdb.pssm │ ├── 1IBR.B.pdb.pssm │ ├── 1IRA.A.pdb.pssm │ ├── 1IRA.B.pdb.pssm │ ├── 1J2J.A.pdb.pssm │ ├── 1J2J.B.pdb.pssm │ ├── 1J2J_282w.A.pdb.pssm │ ├── 1J2J_282w.B.pdb.pssm │ ├── 1JIW.A.pdb.pssm │ ├── 1JIW.B.pdb.pssm │ ├── 1JK9.A.pdb.pssm │ ├── 1JK9.B.pdb.pssm │ ├── 1JTG.A.pdb.pssm │ ├── 1JTG.B.pdb.pssm │ ├── 1JTG_259w.A.pdb.pssm │ ├── 1JTG_259w.B.pdb.pssm │ ├── 1JTG_315w.A.pdb.pssm │ ├── 1JTG_315w.B.pdb.pssm │ ├── 1JTG_358w.A.pdb.pssm │ ├── 1JTG_358w.B.pdb.pssm │ ├── 1KAC.A.pdb.pssm │ ├── 1KAC.B.pdb.pssm │ ├── 1KAC_317w.A.pdb.pssm │ ├── 1KAC_317w.B.pdb.pssm │ ├── 1KTZ.A.pdb.pssm │ ├── 1KTZ.B.pdb.pssm │ ├── 1KXP.A.pdb.pssm │ ├── 1KXP.B.pdb.pssm │ ├── 1KXQ.A.pdb.pssm │ ├── 1KXQ.B.pdb.pssm │ ├── 1LFD.A.pdb.pssm │ ├── 1LFD.B.pdb.pssm │ ├── 1LFD_202w.A.pdb.pssm │ ├── 1LFD_202w.B.pdb.pssm │ ├── 1LFD_272w.A.pdb.pssm │ ├── 1LFD_272w.B.pdb.pssm │ ├── 1LFD_292w.A.pdb.pssm │ ├── 1LFD_292w.B.pdb.pssm │ ├── 1LFD_359w.A.pdb.pssm │ ├── 1LFD_359w.B.pdb.pssm │ ├── 1LFD_368w.A.pdb.pssm │ ├── 1LFD_368w.B.pdb.pssm │ ├── 1M10.A.pdb.pssm │ ├── 1M10.B.pdb.pssm │ ├── 1MAH.A.pdb.pssm │ ├── 1MAH.B.pdb.pssm │ ├── 1MAH_241w.A.pdb.pssm │ ├── 1MAH_241w.B.pdb.pssm │ ├── 1MQ8.A.pdb.pssm │ ├── 1MQ8.B.pdb.pssm │ ├── 1NW9.A.pdb.pssm │ ├── 1NW9.B.pdb.pssm │ ├── 1NW9_12w.A.pdb.pssm │ ├── 1NW9_12w.B.pdb.pssm │ ├── 1NW9_70w.A.pdb.pssm │ ├── 1NW9_70w.B.pdb.pssm │ ├── 1OC0.A.pdb.pssm │ ├── 1OC0.B.pdb.pssm │ ├── 1OC0_281w.A.pdb.pssm │ ├── 1OC0_281w.B.pdb.pssm │ ├── 1OPH.A.pdb.pssm │ ├── 1OPH.B.pdb.pssm │ ├── 1OYV.A.pdb.pssm │ ├── 1OYV.B.pdb.pssm │ ├── 1OYV_77w.A.pdb.pssm │ ├── 1OYV_77w.B.pdb.pssm │ ├── 1PPE.A.pdb.pssm │ ├── 1PPE.B.pdb.pssm │ ├── 1PVH.A.pdb.pssm │ ├── 1PVH.B.pdb.pssm │ ├── 1PVH_151w.A.pdb.pssm │ ├── 1PVH_151w.B.pdb.pssm │ ├── 1PVH_394w.A.pdb.pssm │ ├── 1PVH_394w.B.pdb.pssm │ ├── 1PXV.A.pdb.pssm │ ├── 1PXV.B.pdb.pssm │ ├── 1QA9.A.pdb.pssm │ ├── 1QA9.B.pdb.pssm │ ├── 1R0R.A.pdb.pssm │ ├── 1R0R.B.pdb.pssm │ ├── 1R0R_282w.A.pdb.pssm │ ├── 1R0R_282w.B.pdb.pssm │ ├── 1R6Q.A.pdb.pssm │ ├── 1R6Q.B.pdb.pssm │ ├── 1R6Q_170w.A.pdb.pssm │ ├── 1R6Q_170w.B.pdb.pssm │ ├── 1R8S.A.pdb.pssm │ ├── 1R8S.B.pdb.pssm │ ├── 1S1Q.A.pdb.pssm │ ├── 1S1Q.B.pdb.pssm │ ├── 1S1Q_336w.A.pdb.pssm │ ├── 1S1Q_336w.B.pdb.pssm │ ├── 1S1Q_77w.A.pdb.pssm │ ├── 1S1Q_77w.B.pdb.pssm │ ├── 1SBB.A.pdb.pssm │ ├── 1SBB.B.pdb.pssm │ ├── 1SYX.A.pdb.pssm │ ├── 1SYX.B.pdb.pssm │ ├── 1T6B.A.pdb.pssm │ ├── 1T6B.B.pdb.pssm │ ├── 1TMQ.A.pdb.pssm │ ├── 1TMQ.B.pdb.pssm │ ├── 1TMQ_10w.A.pdb.pssm │ ├── 1TMQ_10w.B.pdb.pssm │ ├── 1US7.A.pdb.pssm │ ├── 1US7.B.pdb.pssm │ ├── 1US7_301w.A.pdb.pssm │ ├── 1US7_301w.B.pdb.pssm │ ├── 1WQ1.A.pdb.pssm │ ├── 1WQ1.B.pdb.pssm │ ├── 1WQ1_348w.A.pdb.pssm │ ├── 1WQ1_348w.B.pdb.pssm │ ├── 1XD3.A.pdb.pssm │ ├── 1XD3.B.pdb.pssm │ ├── 1XQS.A.pdb.pssm │ ├── 1XQS.B.pdb.pssm │ ├── 1XQS_217w.A.pdb.pssm │ ├── 1XQS_217w.B.pdb.pssm │ ├── 1XQS_32w.A.pdb.pssm │ ├── 1XQS_32w.B.pdb.pssm │ ├── 1Y64.A.pdb.pssm │ ├── 1Y64.B.pdb.pssm │ ├── 1YVB.A.pdb.pssm │ ├── 1YVB.B.pdb.pssm │ ├── 1YVB_104w.A.pdb.pssm │ ├── 1YVB_104w.B.pdb.pssm │ ├── 1YVB_105w.A.pdb.pssm │ ├── 1YVB_105w.B.pdb.pssm │ ├── 1YVB_349w.A.pdb.pssm │ ├── 1YVB_349w.B.pdb.pssm │ ├── 1Z0K.A.pdb.pssm │ ├── 1Z0K.B.pdb.pssm │ ├── 1Z0K_324w.A.pdb.pssm │ ├── 1Z0K_324w.B.pdb.pssm │ ├── 1Z0K_93w.A.pdb.pssm │ ├── 1Z0K_93w.B.pdb.pssm │ ├── 1Z5Y.A.pdb.pssm │ ├── 1Z5Y.B.pdb.pssm │ ├── 1Z5Y_203w.A.pdb.pssm │ ├── 1Z5Y_203w.B.pdb.pssm │ ├── 1Z5Y_261w.A.pdb.pssm │ ├── 1Z5Y_261w.B.pdb.pssm │ ├── 1ZHH.A.pdb.pssm │ ├── 1ZHH.B.pdb.pssm │ ├── 1ZHH_319w.A.pdb.pssm │ ├── 1ZHH_319w.B.pdb.pssm │ ├── 1ZHH_364w.A.pdb.pssm │ ├── 1ZHH_364w.B.pdb.pssm │ ├── 1ZHI.A.pdb.pssm │ ├── 1ZHI.B.pdb.pssm │ ├── 1ZHI_114w.A.pdb.pssm │ ├── 1ZHI_114w.B.pdb.pssm │ ├── 1ZHI_295w.A.pdb.pssm │ ├── 1ZHI_295w.B.pdb.pssm │ ├── 1ZHI_316w.A.pdb.pssm │ ├── 1ZHI_316w.B.pdb.pssm │ ├── 1ZLI.A.pdb.pssm │ ├── 1ZLI.B.pdb.pssm │ ├── 1ZM4.A.pdb.pssm │ ├── 1ZM4.B.pdb.pssm │ ├── 2A5T.A.pdb.pssm │ ├── 2A5T.B.pdb.pssm │ ├── 2A5T_145w.A.pdb.pssm │ ├── 2A5T_145w.B.pdb.pssm │ ├── 2A9K.A.pdb.pssm │ ├── 2A9K.B.pdb.pssm │ ├── 2A9K_214w.A.pdb.pssm │ ├── 2A9K_214w.B.pdb.pssm │ ├── 2A9K_346w.A.pdb.pssm │ ├── 2A9K_346w.B.pdb.pssm │ ├── 2ABZ.A.pdb.pssm │ ├── 2ABZ.B.pdb.pssm │ ├── 2ABZ_330w.A.pdb.pssm │ ├── 2ABZ_330w.B.pdb.pssm │ ├── 2AJF.A.pdb.pssm │ ├── 2AJF.B.pdb.pssm │ ├── 2AYO.A.pdb.pssm │ ├── 2AYO.B.pdb.pssm │ ├── 2AYO_215w.A.pdb.pssm │ ├── 2AYO_215w.B.pdb.pssm │ ├── 2B42.A.pdb.pssm │ ├── 2B42.B.pdb.pssm │ ├── 2BTF.A.pdb.pssm │ ├── 2BTF.B.pdb.pssm │ ├── 2BTF_133w.A.pdb.pssm │ ├── 2BTF_133w.B.pdb.pssm │ ├── 2BTF_33w.A.pdb.pssm │ ├── 2BTF_33w.B.pdb.pssm │ ├── 2BTF_383w.A.pdb.pssm │ ├── 2BTF_383w.B.pdb.pssm │ ├── 2C0L.A.pdb.pssm │ ├── 2C0L.B.pdb.pssm │ ├── 2CFH.A.pdb.pssm │ ├── 2CFH.B.pdb.pssm │ ├── 2FJU.A.pdb.pssm │ ├── 2FJU.B.pdb.pssm │ ├── 2FJU_194w.A.pdb.pssm │ ├── 2FJU_194w.B.pdb.pssm │ ├── 2G77.A.pdb.pssm │ ├── 2G77.B.pdb.pssm │ ├── 2H7V.A.pdb.pssm │ ├── 2H7V.B.pdb.pssm │ ├── 2HLE.A.pdb.pssm │ ├── 2HLE.B.pdb.pssm │ ├── 2HLE_185w.A.pdb.pssm │ ├── 2HLE_185w.B.pdb.pssm │ ├── 2HLE_39w.A.pdb.pssm │ ├── 2HLE_39w.B.pdb.pssm │ ├── 2HLE_400w.A.pdb.pssm │ ├── 2HLE_400w.B.pdb.pssm │ ├── 2HQS.A.pdb.pssm │ ├── 2HQS.B.pdb.pssm │ ├── 2HQS_331w.A.pdb.pssm │ ├── 2HQS_331w.B.pdb.pssm │ ├── 2HRK.A.pdb.pssm │ ├── 2HRK.B.pdb.pssm │ ├── 2I25.A.pdb.pssm │ ├── 2I25.B.pdb.pssm │ ├── 2I9B.A.pdb.pssm │ ├── 2I9B.B.pdb.pssm │ ├── 2IDO.A.pdb.pssm │ ├── 2IDO.B.pdb.pssm │ ├── 2J0T.A.pdb.pssm │ ├── 2J0T.B.pdb.pssm │ ├── 2J7P.A.pdb.pssm │ ├── 2J7P.B.pdb.pssm │ ├── 2J7P_255w.A.pdb.pssm │ ├── 2J7P_255w.B.pdb.pssm │ ├── 2J7P_331w.A.pdb.pssm │ ├── 2J7P_331w.B.pdb.pssm │ ├── 2NZ8.A.pdb.pssm │ ├── 2NZ8.B.pdb.pssm │ ├── 2O3B.A.pdb.pssm │ ├── 2O3B.B.pdb.pssm │ ├── 2O3B_137w.A.pdb.pssm │ ├── 2O3B_137w.B.pdb.pssm │ ├── 2O3B_366w.A.pdb.pssm │ ├── 2O3B_366w.B.pdb.pssm │ ├── 2O3B_386w.A.pdb.pssm │ ├── 2O3B_386w.B.pdb.pssm │ ├── 2O8V.A.pdb.pssm │ ├── 2O8V.B.pdb.pssm │ ├── 2OOB.A.pdb.pssm │ ├── 2OOB.B.pdb.pssm │ ├── 2OOB_76w.A.pdb.pssm │ ├── 2OOB_76w.B.pdb.pssm │ ├── 2OT3.A.pdb.pssm │ ├── 2OT3.B.pdb.pssm │ ├── 2OUL.A.pdb.pssm │ ├── 2OUL.B.pdb.pssm │ ├── 2OUL_242w.A.pdb.pssm │ ├── 2OUL_242w.B.pdb.pssm │ ├── 2OZA.A.pdb.pssm │ ├── 2OZA.B.pdb.pssm │ ├── 2PCC.A.pdb.pssm │ ├── 2PCC.B.pdb.pssm │ ├── 2PCC_166w.A.pdb.pssm │ ├── 2PCC_166w.B.pdb.pssm │ ├── 2PCC_182w.A.pdb.pssm │ ├── 2PCC_182w.B.pdb.pssm │ ├── 2PCC_257w.A.pdb.pssm │ ├── 2PCC_257w.B.pdb.pssm │ ├── 2SIC.A.pdb.pssm │ ├── 2SIC.B.pdb.pssm │ ├── 2SIC_168w.A.pdb.pssm │ ├── 2SIC_168w.B.pdb.pssm │ ├── 2SIC_41w.A.pdb.pssm │ ├── 2SIC_41w.B.pdb.pssm │ ├── 2SIC_88w.A.pdb.pssm │ ├── 2SIC_88w.B.pdb.pssm │ ├── 2SNI.A.pdb.pssm │ ├── 2SNI.B.pdb.pssm │ ├── 2VDB.A.pdb.pssm │ ├── 2VDB.B.pdb.pssm │ ├── 2Z0E.A.pdb.pssm │ ├── 2Z0E.B.pdb.pssm │ ├── 3CPH.A.pdb.pssm │ ├── 3CPH.B.pdb.pssm │ ├── 3CPH_262w.A.pdb.pssm │ ├── 3CPH_262w.B.pdb.pssm │ ├── 3D5S.A.pdb.pssm │ ├── 3D5S.B.pdb.pssm │ ├── 3D5S_188w.A.pdb.pssm │ ├── 3D5S_188w.B.pdb.pssm │ ├── 3D5S_258w.A.pdb.pssm │ ├── 3D5S_258w.B.pdb.pssm │ ├── 3D5S_82w.A.pdb.pssm │ ├── 3D5S_82w.B.pdb.pssm │ ├── 3SGQ.A.pdb.pssm │ ├── 3SGQ.B.pdb.pssm │ ├── 3SGQ_274w.A.pdb.pssm │ ├── 3SGQ_274w.B.pdb.pssm │ ├── 4CPA.A.pdb.pssm │ ├── 4CPA.B.pdb.pssm │ ├── 7CEI.A.pdb.pssm │ ├── 7CEI.B.pdb.pssm │ ├── 7CEI_127w.A.pdb.pssm │ ├── 7CEI_127w.B.pdb.pssm │ ├── 7CEI_169w.A.pdb.pssm │ ├── 7CEI_169w.B.pdb.pssm │ ├── 7CEI_321w.A.pdb.pssm │ ├── 7CEI_321w.B.pdb.pssm │ ├── 7CEI_331w.A.pdb.pssm │ ├── 7CEI_331w.B.pdb.pssm │ ├── 7CEI_55w.A.pdb.pssm │ ├── 7CEI_55w.B.pdb.pssm │ ├── BOYV.A.pdb.pssm │ └── BOYV.B.pdb.pssm ├── iScore ├── __init__.py ├── __version__.py ├── energetic │ ├── __init__.py │ ├── energy.py │ ├── forcefield │ │ ├── patch.top │ │ ├── protein-allhdg5-4_new.param │ │ └── protein-allhdg5-4_new.top │ ├── haddock_energy.py │ └── internal_energy.py ├── function │ ├── __init__.py │ └── score.py ├── graphrank │ ├── __init__.py │ ├── cuda │ │ ├── Makefile │ │ ├── cuda_kernel.cu │ │ ├── kernel.hpp │ │ └── main.cu │ ├── graph.py │ ├── kernel.py │ ├── process.py │ └── rank.py ├── h5x │ ├── __init__.py │ ├── baseimport.py │ └── menu.py ├── model │ └── training_set.tar.gz └── process │ ├── __init__.py │ └── plot.py ├── image ├── component_overview_horizontal.png ├── graph.png └── workflow.png ├── makefile ├── setup.py ├── test ├── graph │ ├── 1ATN.A.pdb.pssm │ ├── 1ATN.B.pdb.pssm │ ├── 1ATN.mat │ ├── 1ATN.pckl │ └── 1ATN.pdb ├── graph_notalligned │ ├── 1ATN.A.pssm │ ├── 1ATN.B.pssm │ ├── 1ATN.mat │ ├── 1ATN.pckl │ └── 1ATN.pdb ├── kernel │ ├── check │ │ ├── 1IRA.mat │ │ ├── 2OZA.mat │ │ └── K.mat │ ├── pdb │ │ ├── 1IRA.pdb │ │ └── 2OZA.pdb │ ├── pssm │ │ ├── 1IRA.A.pdb.pssm │ │ ├── 1IRA.B.pdb.pssm │ │ ├── 2OZA.A.pdb.pssm │ │ └── 2OZA.B.pdb.pssm │ ├── testID.lst │ └── trainID.lst ├── process │ ├── caseID.lst │ └── iScorePredict.dat ├── rank │ ├── test │ │ ├── pdb │ │ │ ├── 1ACB_1w.pdb │ │ │ ├── 1ACB_2w.pdb │ │ │ ├── 1ACB_3w.pdb │ │ │ ├── 1ACB_4w.pdb │ │ │ └── 1ACB_5w.pdb │ │ └── pssm │ │ │ ├── 1ACB_1w.A.pdb.pssm │ │ │ ├── 1ACB_1w.B.pdb.pssm │ │ │ ├── 1ACB_2w.A.pdb.pssm │ │ │ ├── 1ACB_2w.B.pdb.pssm │ │ │ ├── 1ACB_3w.A.pdb.pssm │ │ │ ├── 1ACB_3w.B.pdb.pssm │ │ │ ├── 1ACB_4w.A.pdb.pssm │ │ │ ├── 1ACB_4w.B.pdb.pssm │ │ │ ├── 1ACB_5w.A.pdb.pssm │ │ │ └── 1ACB_5w.B.pdb.pssm │ └── 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