├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── alphaspace2 ├── Cluster.py ├── Community.py ├── Configs.py ├── Features.py ├── Snapshot.py ├── Trajectory.py ├── View.py ├── VinaScoring.py ├── __init__.py ├── data │ ├── AS_Chimera_alpha.py │ ├── AS_Chimera_beta.py │ ├── amber_types_fine.dat │ ├── autodock_atom_type_info.dat │ ├── colors_chimera.txt │ ├── colors_table.txt │ ├── hp_types_dict.dat │ ├── typing_from_pdb.dat │ └── vina_params.dat └── functions.py ├── bin └── alphaspace2 ├── cookbooks ├── 1_FCTM_bclxl_bak.ipynb ├── 2_Compare.ipynb ├── 3_Beta_cluster_features.ipynb ├── 4_Ligand-optimizability.ipynb ├── 5_CDK2_communities_analysis.ipynb ├── DTM.ipynb ├── DataSet │ ├── Beta_Cluster_features │ │ ├── ligand_1c70.pdb │ │ ├── ligand_1hvi.pdb │ │ ├── ligand_1hvj.pdb │ │ ├── ligand_1izh.pdb │ │ ├── ligand_1pro.pdb │ │ ├── ligand_1siv.pdb │ │ ├── ligand_2i0a.pdb │ │ ├── ligand_2psv.pdb │ │ ├── ligand_2q5k.pdb │ │ ├── ligand_3lzu.pdb │ │ ├── protein_1c70.pdb │ │ ├── protein_1hvi.pdb │ │ ├── protein_1hvj.pdb │ │ ├── protein_1izh.pdb │ │ ├── protein_1pro.pdb │ │ ├── protein_1siv.pdb │ │ ├── protein_2i0a.pdb │ │ ├── protein_2psv.pdb │ │ ├── protein_2q5k.pdb │ │ └── protein_3lzu.pdb │ ├── Binding_Site_comparison │ │ ├── estrogen_receptor │ │ │ ├── protein_2b1z.pdb │ │ │ ├── protein_2p15.pdb │ │ │ ├── protein_2pog.pdb │ │ │ ├── protein_2q70.pdb │ │ │ ├── protein_2yja.pdb │ │ │ ├── protein_3uud.pdb │ │ │ ├── protein_4mg8.pdb │ │ │ ├── protein_4pps.pdb │ │ │ ├── protein_4pxm.pdb │ │ │ ├── protein_4tv1.pdb │ │ │ ├── protein_lig_2b1z.pdb │ │ │ ├── protein_lig_2p15.pdb │ │ │ ├── protein_lig_2pog.pdb │ │ │ ├── protein_lig_2q70.pdb │ │ │ ├── protein_lig_2yja.pdb │ │ │ ├── protein_lig_3uud.pdb │ │ │ ├── protein_lig_4mg8.pdb │ │ │ ├── protein_lig_4pps.pdb │ │ │ ├── protein_lig_4pxm.pdb │ │ │ ├── protein_lig_4tv1.pdb │ │ │ └── representative_ligand.pdb │ │ ├── pka │ │ │ ├── protein_1sve.pdb │ │ │ ├── protein_1xh5.pdb │ │ │ ├── protein_2c1a.pdb │ │ │ ├── protein_2erz.pdb │ │ │ ├── protein_2f7e.pdb │ │ │ ├── protein_2f7x.pdb │ │ │ ├── protein_2gfc.pdb │ │ │ ├── protein_2jds.pdb │ │ │ ├── protein_2oh0.pdb │ │ │ ├── protein_2vo7.pdb │ │ │ ├── protein_lig_1sve.pdb │ │ │ ├── protein_lig_1xh5.pdb │ │ │ ├── protein_lig_2c1a.pdb │ │ │ ├── protein_lig_2erz.pdb │ │ │ ├── protein_lig_2f7e.pdb │ │ │ ├── protein_lig_2f7x.pdb │ │ │ ├── protein_lig_2gfc.pdb │ │ │ ├── protein_lig_2jds.pdb │ │ │ ├── protein_lig_2oh0.pdb │ │ │ ├── protein_lig_2vo7.pdb │ │ │ └── representative_ligand.pdb │ │ └── protease │ │ │ ├── protein_1c70.pdb │ │ │ ├── protein_1hvi.pdb │ │ │ ├── protein_1hvj.pdb │ │ │ ├── protein_1izh.pdb │ │ │ ├── protein_1pro.pdb │ │ │ ├── protein_1siv.pdb │ │ │ ├── protein_2i0a.pdb │ │ │ ├── protein_2psv.pdb │ │ │ ├── protein_2q5k.pdb │ │ │ ├── protein_3lzu.pdb │ │ │ ├── protein_lig_1c70.pdb │ │ │ ├── protein_lig_1hvi.pdb │ │ │ ├── protein_lig_1hvj.pdb │ │ │ ├── protein_lig_1izh.pdb │ │ │ ├── protein_lig_1pro.pdb │ │ │ ├── protein_lig_1siv.pdb │ │ │ ├── protein_lig_2i0a.pdb │ │ │ ├── protein_lig_2psv.pdb │ │ │ ├── protein_lig_2q5k.pdb │ │ │ ├── protein_lig_3lzu.pdb │ │ │ └── representative_ligand.pdb │ ├── CDK2_Communities │ │ ├── cdk2_prot.pdb │ │ └── cdk2_prot.pdbqt │ ├── CryptoSite_set │ │ ├── 0 │ │ │ ├── apo │ │ │ │ └── 3che │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2iuz │ │ │ │ └── prot_lig.pdb │ │ ├── 1 │ │ │ ├── apo │ │ │ │ └── 2aka │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1yv3 │ │ │ │ └── prot_lig.pdb │ │ ├── 2 │ │ │ ├── apo │ │ │ │ └── 2gfc │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2jds │ │ │ │ └── prot_lig.pdb │ │ ├── 3 │ │ │ ├── apo │ │ │ │ └── 1alb │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1lic │ │ │ │ └── prot_lig.pdb │ │ ├── 4 │ │ │ ├── apo │ │ │ │ └── 1nep │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2hka │ │ │ │ └── prot_lig.pdb │ │ ├── 5 │ │ │ ├── apo │ │ │ │ └── 3mn9 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3eks │ │ │ │ └── prot_lig.pdb │ │ ├── 6 │ │ │ ├── apo │ │ │ │ └── 1alv │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1nx3 │ │ │ │ └── prot_lig.pdb │ │ ├── 7 │ │ │ ├── apo │ │ │ │ └── 2yqc │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2yqs │ │ │ │ └── prot_lig.pdb │ │ ├── 8 │ │ │ ├── apo │ │ │ │ └── 2qfo │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2wi7 │ │ │ │ └── prot_lig.pdb │ │ ├── 9 │ │ │ ├── apo │ │ │ │ └── 1rtc │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1br6 │ │ │ │ └── prot_lig.pdb │ │ ├── 10 │ │ │ ├── apo │ │ │ │ └── 1rdw │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1j6z │ │ │ │ └── prot_lig.pdb │ │ ├── 11 │ │ │ ├── apo │ │ │ │ └── 1tqo │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1tr5 │ │ │ │ └── prot_lig.pdb │ │ ├── 12 │ │ │ ├── apo │ │ │ │ └── 3puw │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1fqc │ │ │ │ └── prot_lig.pdb │ │ ├── 13 │ │ │ ├── apo │ │ │ │ └── 3l7u │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2hvd │ │ │ │ └── prot_lig.pdb │ │ ├── 14 │ │ │ ├── apo │ │ │ │ └── 1r1w │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3f82 │ │ │ │ └── prot_lig.pdb │ │ ├── 15 │ │ │ ├── apo │ │ │ │ └── 1g4e │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1g67 │ │ │ │ └── prot_lig.pdb │ │ ├── 16 │ │ │ ├── apo │ │ │ │ └── 3f74 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3bqm │ │ │ │ └── prot_lig.pdb │ │ ├── 17 │ │ │ ├── apo │ │ │ │ └── 1my1 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ftl │ │ │ │ └── prot_lig.pdb │ │ ├── 18 │ │ │ ├── apo │ │ │ │ └── 2wgq │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1d6y │ │ │ │ └── prot_lig.pdb │ │ ├── 19 │ │ │ ├── apo │ │ │ │ └── 1dub │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ey3 │ │ │ │ └── prot_lig.pdb │ │ ├── 20 │ │ │ ├── apo │ │ │ │ └── 1pzt │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1pzy │ │ │ │ └── prot_lig.pdb │ │ ├── 21 │ │ │ ├── apo │ │ │ │ └── 1xmg │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1xvc │ │ │ │ └── prot_lig.pdb │ │ ├── 22 │ │ │ ├── apo │ │ │ │ └── 1imf │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1imb │ │ │ │ └── prot_lig.pdb │ │ ├── 23 │ │ │ ├── apo │ │ │ │ └── 2ax9 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2piq │ │ │ │ └── prot_lig.pdb │ │ ├── 24 │ │ │ ├── apo │ │ │ │ └── 1exm │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ha3 │ │ │ │ └── prot_lig.pdb │ │ ├── 25 │ │ │ ├── apo │ │ │ │ └── 3kqa │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3lth │ │ │ │ └── prot_lig.pdb │ │ ├── 26 │ │ │ ├── apo │ │ │ │ └── 2bf3 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3dhh │ │ │ │ └── prot_lig.pdb │ │ ├── 27 │ │ │ ├── apo │ │ │ │ └── 1cll │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ctr │ │ │ │ └── prot_lig.pdb │ │ ├── 28 │ │ │ ├── apo │ │ │ │ └── 3h5r │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3h9j │ │ │ │ └── prot_lig.pdb │ │ ├── 29 │ │ │ ├── apo │ │ │ │ └── 1ni6 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3hok │ │ │ │ └── prot_lig.pdb │ │ ├── 30 │ │ │ ├── apo │ │ │ │ └── 1qlw │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2wkw │ │ │ │ └── prot_lig.pdb │ │ ├── 31 │ │ │ ├── apo │ │ │ │ └── 1hag │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ghy │ │ │ │ └── prot_lig.pdb │ │ ├── 32 │ │ │ ├── apo │ │ │ │ └── 1ok8 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1oke │ │ │ │ └── prot_lig.pdb │ │ ├── 33 │ │ │ ├── apo │ │ │ │ └── 3dxn │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3hzt │ │ │ │ └── prot_lig.pdb │ │ ├── 34 │ │ │ ├── apo │ │ │ │ └── 1k5h │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2egh │ │ │ │ └── prot_lig.pdb │ │ ├── 35 │ │ │ ├── apo │ │ │ │ └── 1hka │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3ip0 │ │ │ │ └── prot_lig.pdb │ │ ├── 36 │ │ │ ├── apo │ │ │ │ └── 2bu8 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2bu2 │ │ │ │ └── prot_lig.pdb │ │ ├── 37 │ │ │ ├── apo │ │ │ │ └── 2ohg │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2ohv │ │ │ │ └── prot_lig.pdb │ │ ├── 38 │ │ │ ├── apo │ │ │ │ └── 2bls │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3gqz │ │ │ │ └── prot_lig.pdb │ │ ├── 39 │ │ │ ├── apo │ │ │ │ └── 1rhb │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2w5k │ │ │ │ └── prot_lig.pdb │ │ ├── 40 │ │ │ ├── apo │ │ │ │ └── 1ade │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1cib │ │ │ │ └── prot_lig.pdb │ │ ├── 41 │ │ │ ├── apo │ │ │ │ └── 1ks9 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2ofp │ │ │ │ └── prot_lig.pdb │ │ ├── 42 │ │ │ ├── apo │ │ │ │ └── 1h09 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2ixu │ │ │ │ └── prot_lig.pdb │ │ ├── 43 │ │ │ ├── apo │ │ │ │ └── 3bl9 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3bl7 │ │ │ │ └── prot_lig.pdb │ │ ├── 44 │ │ │ ├── apo │ │ │ │ └── 1bp5 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ryo │ │ │ │ └── prot_lig.pdb │ │ ├── 45 │ │ │ ├── apo │ │ │ │ └── 2q8f │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2q8h │ │ │ │ └── prot_lig.pdb │ │ ├── 46 │ │ │ ├── apo │ │ │ │ └── 2iyt │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2iyq │ │ │ │ └── prot_lig.pdb │ │ ├── 47 │ │ │ ├── apo │ │ │ │ └── 1ex6 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1gky │ │ │ │ └── prot_lig.pdb │ │ ├── 48 │ │ │ ├── apo │ │ │ │ └── 1rrg │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1s9d │ │ │ │ └── prot_lig.pdb │ │ ├── 49 │ │ │ ├── apo │ │ │ │ └── 1ecj │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ecc │ │ │ │ └── prot_lig.pdb │ │ ├── 50 │ │ │ ├── apo │ │ │ │ └── 2cm2 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2h4k │ │ │ │ └── prot_lig.pdb │ │ ├── 51 │ │ │ ├── apo │ │ │ │ └── 1nuw │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1eyj │ │ │ │ └── prot_lig.pdb │ │ ├── 52 │ │ │ ├── apo │ │ │ │ └── 3cj0 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ ├── 2brl │ │ │ │ └── prot_lig.pdb │ │ │ │ └── 3fqk │ │ │ │ └── prot_lig.pdb │ │ ├── 53 │ │ │ ├── apo │ │ │ │ └── 1uk2 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2gz7 │ │ │ │ └── prot_lig.pdb │ │ ├── 54 │ │ │ ├── apo │ │ │ │ └── 2wgb │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2v57 │ │ │ │ └── prot_lig.pdb │ │ ├── 55 │ │ │ ├── apo │ │ │ │ └── 1hoo │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1cib │ │ │ │ └── prot_lig.pdb │ │ ├── 56 │ │ │ ├── apo │ │ │ │ └── 1fa9 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1l5s │ │ │ │ └── prot_lig.pdb │ │ ├── 57 │ │ │ ├── apo │ │ │ │ └── 1w50 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3ixj │ │ │ │ └── prot_lig.pdb │ │ ├── 58 │ │ │ ├── apo │ │ │ │ └── 3b7d │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2al4 │ │ │ │ └── prot_lig.pdb │ │ ├── 59 │ │ │ ├── apo │ │ │ │ └── 1pkl │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3hqp │ │ │ │ └── prot_lig.pdb │ │ ├── 60 │ │ │ ├── apo │ │ │ │ └── 1k3f │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1u1d │ │ │ │ └── prot_lig.pdb │ │ ├── 61 │ │ │ ├── apo │ │ │ │ └── 1fvr │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2oo8 │ │ │ │ └── prot_lig.pdb │ │ ├── 62 │ │ │ ├── apo │ │ │ │ └── 3hqd │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1q0b │ │ │ │ └── prot_lig.pdb │ │ ├── 63 │ │ │ ├── apo │ │ │ │ └── 2zb1 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2npq │ │ │ │ └── prot_lig.pdb │ │ ├── 64 │ │ │ ├── apo │ │ │ │ └── 3peo │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2bys │ │ │ │ └── prot_lig.pdb │ │ ├── 65 │ │ │ ├── apo │ │ │ │ └── 2brk │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2gir │ │ │ │ └── prot_lig.pdb │ │ ├── 66 │ │ │ ├── apo │ │ │ │ └── 2h4e │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3cfn │ │ │ │ └── prot_lig.pdb │ │ ├── 67 │ │ │ ├── apo │ │ │ │ └── 2cga │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1afq │ │ │ │ └── prot_lig.pdb │ │ ├── 68 │ │ │ ├── apo │ │ │ │ └── 1xcg │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ow3 │ │ │ │ └── prot_lig.pdb │ │ ├── 69 │ │ │ ├── apo │ │ │ │ └── 1fxx │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3hl8 │ │ │ │ └── prot_lig.pdb │ │ ├── 70 │ │ │ ├── apo │ │ │ │ └── 4ake │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1ank │ │ │ │ └── prot_lig.pdb │ │ ├── 71 │ │ │ ├── apo │ │ │ │ └── 3nnu │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3hl7 │ │ │ │ └── prot_lig.pdb │ │ ├── 72 │ │ │ ├── apo │ │ │ │ └── 1a8i │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2ieg │ │ │ │ └── prot_lig.pdb │ │ ├── 73 │ │ │ ├── apo │ │ │ │ └── 1swx │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 2eum │ │ │ │ └── prot_lig.pdb │ │ ├── 74 │ │ │ ├── apo │ │ │ │ └── 2qlr │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3dc1 │ │ │ │ └── prot_lig.pdb │ │ ├── 75 │ │ │ ├── apo │ │ │ │ └── 2f6v │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1t49 │ │ │ │ └── prot_lig.pdb │ │ ├── 76 │ │ │ ├── apo │ │ │ │ └── 1g24 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 1gzf │ │ │ │ └── prot_lig.pdb │ │ ├── 77 │ │ │ ├── apo │ │ │ │ └── 1su4 │ │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ │ └── 3fgo │ │ │ │ └── prot_lig.pdb │ │ └── 78 │ │ │ ├── apo │ │ │ └── 2air │ │ │ │ └── prot_lig.pdb │ │ │ └── holo │ │ │ └── 1za1 │ │ │ └── prot_lig.pdb │ ├── Fragment_to_Lead │ │ ├── ligand_frag_2wi2.pdb │ │ ├── ligand_lead_2wi7.pdb │ │ ├── protein_2wi2.pdb │ │ ├── protein_2wi2.pdbqt │ │ ├── protein_2wi7.pdb │ │ └── protein_2wi7.pdbqt │ ├── Ichihara_set_proteins │ │ ├── Aurora │ │ │ ├── 2w1d │ │ │ │ └── protein_lig.pdb │ │ │ └── 2w1g │ │ │ │ └── protein_lig.pdb │ │ ├── BACE_1 │ │ │ ├── 2ohm │ │ │ │ └── protein_lig.pdb │ │ │ └── 2ohu │ │ │ │ └── protein_lig.pdb │ │ ├── BACE_2 │ │ │ ├── 2v00 │ │ │ │ └── protein_lig.pdb │ │ │ └── 2va7 │ │ │ │ └── protein_lig.pdb │ │ ├── Biotin_cbx │ │ │ ├── 2w70 │ │ │ │ └── protein_lig.pdb │ │ │ └── 2w71 │ │ │ │ └── protein_lig.pdb │ │ ├── CDK2_1 │ │ │ ├── 1vyw │ │ │ │ └── protein_lig.pdb │ │ │ └── 1vyz │ │ │ │ └── protein_lig.pdb │ │ ├── CDK2_2 │ │ │ ├── 2vta │ │ │ │ └── protein_lig.pdb │ │ │ └── 2vu3 │ │ │ │ └── protein_lig.pdb │ │ ├── DPP │ │ │ ├── 3ccb │ │ │ │ └── protein_lig.pdb │ │ │ └── 3ccc │ │ │ │ └── protein_lig.pdb │ │ ├── HSP90_1 │ │ │ ├── 2qfo │ │ │ │ └── protein_lig.pdb │ │ │ └── 2qg0 │ │ │ │ └── protein_lig.pdb │ │ ├── HSP90_2 │ │ │ ├── 3ft5 │ │ │ │ └── protein_lig.pdb │ │ │ └── 3ft8 │ │ │ │ └── protein_lig.pdb │ │ ├── HSP90_3 │ │ │ ├── 2wi2 │ │ │ │ └── protein_lig.pdb │ │ │ └── 2wi7 │ │ │ │ └── protein_lig.pdb │ │ ├── NS5_pmrase │ │ │ ├── 3ciz │ │ │ │ └── protein_lig.pdb │ │ │ └── 3cj5 │ │ │ │ └── protein_lig.pdb │ │ ├── PDE │ │ │ ├── 1y2b │ │ │ │ └── protein_lig.pdb │ │ │ └── 1y2k │ │ │ │ └── protein_lig.pdb │ │ ├── PKB_1 │ │ │ ├── 2uw3 │ │ │ │ └── protein_lig.pdb │ │ │ └── 2uw7 │ │ │ │ └── protein_lig.pdb │ │ ├── PKB_2 │ │ │ ├── 2uvx │ │ │ │ └── protein_lig.pdb │ │ │ └── 2vo6 │ │ │ │ └── protein_lig.pdb │ │ ├── PPAR │ │ │ ├── 3et0 │ │ │ │ └── protein_lig.pdb │ │ │ └── 3et3 │ │ │ │ └── protein_lig.pdb │ │ ├── jak2 │ │ │ ├── 3e62 │ │ │ │ └── protein_lig.pdb │ │ │ └── 3e64 │ │ │ │ └── protein_lig.pdb │ │ ├── lta4h │ │ │ ├── 3fh7 │ │ │ │ └── protein_lig.pdb │ │ │ └── 3fu0 │ │ │ │ └── protein_lig.pdb │ │ ├── p38a_1 │ │ │ ├── 1w84 │ │ │ │ └── protein_lig.pdb │ │ │ └── 1wbt │ │ │ │ └── protein_lig.pdb │ │ ├── p38a_2 │ │ │ ├── 1w7h │ │ │ │ └── protein_lig.pdb │ │ │ └── 1w83 │ │ │ │ └── protein_lig.pdb │ │ └── uPA │ │ │ ├── 2vin │ │ │ └── protein_lig.pdb │ │ │ └── 2viw │ │ │ └── protein_lig.pdb │ └── bcl2 │ │ ├── Bcl2_BAX │ │ ├── beta_pocks_BAX_MODELS.pdb │ │ ├── lig.pdb │ │ ├── prot.pdb │ │ └── prot.pdbqt │ │ ├── BclXL_BAK │ │ ├── AS_Chimera_alpha.py │ │ ├── AS_Chimera_beta.py │ │ ├── bclxl-bak.png │ │ ├── colors_chimera.txt │ │ ├── colors_table.txt │ │ ├── lig.pdb │ │ ├── pdb_out │ │ │ ├── lig.pdb │ │ │ └── prot.pdb │ │ ├── pockets │ │ │ ├── 10_alpha.pdb │ │ │ ├── 10_beta.pdb │ │ │ ├── 1_alpha.pdb │ │ │ ├── 1_beta.pdb │ │ │ ├── 2_alpha.pdb │ │ │ ├── 2_beta.pdb │ │ │ ├── 3_alpha.pdb │ │ │ ├── 3_beta.pdb │ │ │ ├── 4_alpha.pdb │ │ │ ├── 4_beta.pdb │ │ │ ├── 5_alpha.pdb │ │ │ ├── 5_beta.pdb │ │ │ ├── 6_alpha.pdb │ │ │ ├── 6_beta.pdb │ │ │ ├── 7_alpha.pdb │ │ │ ├── 7_beta.pdb │ │ │ ├── 8_alpha.pdb │ │ │ ├── 8_beta.pdb │ │ │ ├── 9_alpha.pdb │ │ │ └── 9_beta.pdb │ │ ├── prot.pdb │ │ └── prot.pdbqt │ │ ├── BclXL_BAX │ │ ├── beta_pocks_BAX_MODELS.pdb │ │ ├── lig.pdb │ │ ├── prot.pdb │ │ └── prot.pdbqt │ │ └── bcl.ipynb └── old_examples │ ├── For_Haotian │ ├── Binding_Site_comparison.ipynb │ ├── CDK2_Communities.ipynb │ ├── Fragment_to_Lead.ipynb │ └── communities.py │ ├── Joseph_bcl2_comparison │ ├── Bcl2_BAX │ │ ├── beta_pocks_BAX_MODELS.pdb │ │ ├── lig.pdb │ │ ├── prot.pdb │ │ └── prot.pdbqt │ ├── BclXL_BAX │ │ ├── beta_pocks_BAX_MODELS.pdb │ │ ├── lig.pdb │ │ ├── prot.pdb │ │ └── prot.pdbqt │ ├── Bcl_comparison.ipynb │ ├── amber_types_fine.dat │ └── beta_usr.py │ └── joseph scripts │ ├── beta_usr.py │ ├── example.py │ ├── geometric_alpha.py │ └── get_geom.py └── setup.py /.gitignore: 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