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Table 1 Protein and PDB ID list of human apoptosis pathway dataset

From: Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods

Protein Name

PDB ID (_Chain)

AIF

1M6I_A

     

AKT1

1UNQ_A

3CQW_A

3O96_A

   

AKT2

1MRV_A

1O6K_A

1O6L_A

1P6S_A

  

AKT3

2X18_A

     

APAF1

1CY5_A

1Z6T_A

2YGS_A

3IZA_A

3YGS_C

 

BCL-2

2W3L_A

2XA0_A

    

BCL-XL

2B48_A

3FDL_A

    

BID

2BID_A

2KBW_B

    

Bax

1F16_A

2G5B_I

2XA0_C

3PK1_B

  

CASP3

1RHQ_A

1RHQ_B

2DKO_A

2DKO_B

2J32_A

 

CASP6

2WDP_A

     

CASP7

1F1J_A

1I4O_A

1I51_A

1I51_B

2QL9_A

2QL9_B

CASP8

1QTN_A

1QTN_B

2FUN_B

3H11_B

  

CASP9

1JXQ_A

1NW9_B

3D9T_C

3YGS_P

  

Calpain1

1ZCM_A

     

Calpain2

1KFU_L

2NQA_A

    

Cn(CHP)

2E30_A

     

Cn(CHP2)

2BEC_A

     

Cn(PPP3CA)

1AUI_A

1MF8_A

2R28_C

3LL8_A

  

Cn(PPP3R1)

1AUI_B

1MF8_B

3LL8_B

   

CytC

1J3S_A

     

DFF40

1IBX_A

     

DFF45

1IBX_B

1IYR_A

    

FADD

1A1W_A

2GF5_A

3EZQ_B

   

FLIP

3H11_A

     

Fas

3EWT_E

3EZQ_A

    

IAP(BIRC2)

3D9T_A

3M1D_A

3MUP_A

   

IAP(BIRC3)

2UVL_A

3EB5_A

3EB6_A

3M0A_D

3M0D_D

 

IAP(BIRC4)

1G73_C

1I4O_C

1I51_E

1NW9_A

2ECG_A

2KNA_A

 

2POI_A

3CM7_C

    

IκBα

1IKN_D

1NFI_E

    

IKK

2JVX_A

3BRT_B

3BRV_B

3CL3_D

3FX0_A

 

IL-1(A)

2ILA_A

     

IL-1(B)

1ITB_A

2NVH_A

3O4O_A

   

IL-1R(1)

1ITB_B

     

IL-1R(RAP)

3O4O_B

     

IL-3

1JLI_A

     

IL-3R

1EGJ_A

     

IRAK2

3MOP_K

     

IRAK4

2NRU_A

3MOP_G

    

MyD88

2JS7_A

3MOP_A

    

NF-κB(NFKB1)

1IKN_C

1NFI_B

1SVC_P

2DBF_A

  

NF-κB(RELA)

1IKN_A

1NFI_A

    

NGF

1WWW_V

2IFG_E

    

PI3K(PIK3CA)

2ENQ_A

2V1Y_A

3HHM_A

   

PI3K(PIK3CG)

1E8Y_A

     

PI3K(PIK3R1)

1A0N_A

1H9O_A

1PBW_A

2IUG_A

2V1Y_B

3HHM_B

 

3I5R_A

     

PI3K(PIK3R2)

2KT1_A

2XS6_A

3MTT_A

   

PRKACA

3AGM_A

     

PRKAR2A

2IZX_A

     

TNFα

1A8M_A

4TSV_A

    

TNF-R1

1EXT_A

1ICH_A

    

TP53

1AIE_A

1OLG_A

1XQH_B

1YC5_B

2B3G_B

2FOO_B

 

2GS0_B

2K8F_B

2VUK_A

3D06_A

3DAB_B

3LW1_P

TRADD

1F3V_A

     

TRAF2

1CZZ_A

1D00_A

1F3V_B

3KNV_A

3M0A_A

3M0D_A

TRAIL

1D4V_B

1DG6_A

1DU3_D

   

TRAIL-R

1D4V_A

1DU3_A

    

TrkA

1HE7_A

1SHC_B

1WWW_X

2IFG_A

  
  1. The abbreviations used are: AIF, apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1); AKT1, RAC-alpha serine/threonine-protein kinase; AKT2, RAC-beta serine/threonine-protein kinase; AKT3, RAC-gamma serine/threonine-protein kinase; APAF1, apoptotic peptidase activating factor 1; BCL-2, B-cell lymphoma 2; BCL-XL, BCL extra-large; BID, BH3 interacting domain death agonist; Bax, BCL-2-associated × protein; CASP3/6/7/8/9, caspase-3/6/7/8/9; Cn(CHP), calcineurin B homologous protein 1; Cn(CHP2), calcineurin B homologous protein 2; Cn(PPP3CA), protein phosphatase 3 catalytic subunit alpha isoform; Cn(PPP3R1), protein phosphatase 3 regulatory subunit 1; CytC, cytochrome C; DFF40, DNA fragmentation factor, 40kDa, beta polypeptide; DFF45, DNA fragmentation factor, 45kDa, alpha polypeptide; FADD, Fas-associated via death domain; FLIP, FLICE/CASP8 inhibitory protein (CASP8 and FADD-like apoptosis regulator, CFLAR); Fas, tumor necrosis factor receptor (TNF) superfamily member 6; IAP, inhibitor of apoptosis; BIRC2/3/4, baculoviral IAP repeat-containing protein 2/3/4; IκBα, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; IKK, inhibitor of nuclear factor kappa-B kinase; IL-1(A), interleukin-1 alpha; IL-1(B), interleukin-1 beta; IL-1R(1), type 1 interleukin-1 receptor; IL-1R(RAP), interleukin-1 receptor accessory protein; IL-3, interleukin-3; IL-3R, interleukin-3 receptor; IRAK2/4, interleukin-1 receptor-associated kinase 2/4; MyD88, myeloid differentiation primary response protein MyD88; NF-κB(NFKB1), nuclear factor of kappa light polypeptide gene enhancer in B-cells; NF-κB(RELA), nuclear factor of kappa light polypeptide gene enhancer in B-cells 3; NGF, nerve growth factor (beta polypeptide); PI3K, phosphatidylinositide 3-kinase; PIK3CA, PI3K subunit alpha; PIK3CG, PI3K subunit gamma; PIK3R1, PI3K regulatory subunit alpha; PIK3R2, PI3K regulatory subunit beta; PRKACA, cyclic adenosine monophosphate (cAMP)-dependent protein kinase catalytic subunit alpha; PRKAR2A, cAMP-dependent protein kinase type II-alpha regulatory subunit; TNFα, tumor necrosis factor; TNF-R1, TNF receptor superfamily member 1A; TP53, cellular tumor antigen p53; TRADD, TNF receptor type 1-associated death domain protein; TRAF2, TNF receptor-associated factor 2; TRAIL, TNF receptor superfamily member 10; TRAIL-R, TNF receptor superfamily member 10B; TrkA, neurotrophic tyrosine kinase receptor type 1.