├── CADD_old_school ├── README.MD └── kras_virtual_screening │ ├── README.md │ └── similarity_search │ ├── kras8act.png │ ├── kras8act_ChemDiv_Sim_Search.sdf │ ├── kras8act_ChemDiv_Sim_Search_Odin.csv │ ├── kras8act_Specs_Sim_Search.sdf │ ├── kras8act_Specs_Sim_Search_Odin.csv │ ├── kras_active_sim_search │ ├── 0_chemdiv_sim_100.sdf │ ├── 0_specs_sim_100.sdf │ ├── 1_chemdiv_sim_100.sdf │ ├── 1_specs_sim_100.sdf │ ├── 2_chemdiv_sim_100.sdf │ ├── 2_specs_sim_100.sdf │ ├── 3_chemdiv_sim_100.sdf │ ├── 3_specs_sim_100.sdf │ ├── 4_chemdiv_sim_100.sdf │ ├── 4_specs_sim_100.sdf │ ├── 5_chemdiv_sim_100.sdf │ ├── 5_specs_sim_100.sdf │ ├── 6_chemdiv_sim_100.sdf │ ├── 6_specs_sim_100.sdf │ ├── 7_chemdiv_sim_100.sdf │ └── 7_specs_sim_100.sdf │ ├── kras_active_sim_search_pdf │ ├── 0_chemdiv_sim_100.pdf │ ├── 0_specs_sim_100.pdf │ ├── 1_chemdiv_sim_100.pdf │ ├── 1_specs_sim_100.pdf │ ├── 2_chemdiv_sim_100.pdf │ ├── 2_specs_sim_100.pdf │ ├── 3_chemdiv_sim_100.pdf │ ├── 3_specs_sim_100.pdf │ ├── 4_chemdiv_sim_100.pdf │ ├── 4_specs_sim_100.pdf │ ├── 5_chemdiv_sim_100.pdf │ ├── 5_specs_sim_100.pdf │ ├── 6_chemdiv_sim_100.pdf │ ├── 6_specs_sim_100.pdf │ ├── 7_chemdiv_sim_100.pdf │ └── 7_specs_sim_100.pdf │ └── kras_analysis.ipynb ├── README.md ├── biomolecules ├── protein │ ├── fix_cyclic_peptide.py │ ├── pdb_blog │ │ ├── 4gv1_alpha.pdb │ │ ├── 4gv1_ori.sdf │ │ ├── 4gv1_protein.pdb │ │ ├── 4rn0 │ │ │ ├── 4rn0_pocket10.pdb │ │ │ └── test.sdf │ │ ├── README.md │ │ ├── af_pocket.pdb │ │ ├── af_pocket_out │ │ │ ├── af_pocket.tcl │ │ │ ├── af_pocket_.pml │ │ │ ├── af_pocket_PYMOL.sh │ │ │ ├── af_pocket_VMD.sh │ │ │ ├── af_pocket_info.txt │ │ │ ├── af_pocket_out.pdb │ │ │ ├── af_pocket_out.png │ │ │ ├── af_pocket_out_lig.png │ │ │ ├── af_pocket_pockets.pqr │ │ │ └── pockets │ │ │ │ ├── pocket1_atm.pdb │ │ │ │ ├── pocket1_vert.pqr │ │ │ │ ├── pocket2_atm.pdb │ │ │ │ ├── pocket2_vert.pqr │ │ │ │ ├── pocket3_atm.pdb │ │ │ │ ├── pocket3_vert.pqr │ │ │ │ ├── pocket4_atm.pdb │ │ │ │ ├── pocket4_vert.pqr │ │ │ │ ├── pocket5_atm.pdb │ │ │ │ └── pocket5_vert.pqr │ │ ├── alphafold_utils.py │ │ ├── compute_volume.ipynb │ │ ├── copocket_extraction.py │ │ ├── cry_pocket.pdb │ │ ├── disulfide.py │ │ ├── figures │ │ │ ├── interaction_figure.png │ │ │ └── ligand_extract.png │ │ ├── ligand_extraction │ │ │ ├── extract_ligand.py │ │ │ └── seperate_pro_lig.ipynb │ │ ├── pdb_utils.py │ │ └── protein_ligand_interaction.py │ └── protein_utils.py └── small_molecule │ ├── bond.ipynb │ ├── bond_adding.py │ ├── chemical_space │ ├── README.md │ ├── pca_tsne │ │ ├── contour_point.png │ │ ├── crossdock_mols.txt │ │ ├── moses2.txt │ │ ├── pca.png │ │ ├── pca_and_tsne.ipynb │ │ └── t-SNE.png │ └── tmap │ │ ├── 1w_h_acceptors.png │ │ ├── creat_csv_4tmap.py │ │ ├── drugbank.csv │ │ ├── drugbank.py │ │ └── lipinski.py │ ├── docking │ ├── __pycache__ │ │ ├── chem.cpython-39.pyc │ │ └── surflex.cpython-39.pyc │ ├── chem.py │ ├── gnina.py │ ├── ledock.py │ ├── pydocking │ │ ├── README.MD │ │ ├── docking │ │ │ ├── __pycache__ │ │ │ │ ├── chem.cpython-39.pyc │ │ │ │ ├── gnina.cpython-39.pyc │ │ │ │ ├── ledock.cpython-39.pyc │ │ │ │ ├── qvina.cpython-39.pyc │ │ │ │ ├── rdock.cpython-39.pyc │ │ │ │ ├── smina.cpython-39.pyc │ │ │ │ └── surflex.cpython-39.pyc │ │ │ ├── chem.py │ │ │ ├── gnina.py │ │ │ ├── ledock.py │ │ │ ├── qvina.py │ │ │ ├── rdock.py │ │ │ ├── rosetta_ligand.py │ │ │ ├── smina.py │ │ │ └── surflex.py │ │ └── docking_all.ipynb │ ├── qvina.py │ ├── rdock.py │ ├── rosetta_ligand.py │ ├── smina.py │ └── surflex.py │ ├── openeye │ ├── README.md │ ├── case_examples │ │ ├── aliphatic_core.png │ │ ├── aliphatic_core.sdf │ │ ├── bondtop_core.png │ │ ├── bondtop_core.sdf │ │ ├── frag2.png │ │ ├── sim_searched.png │ │ ├── sim_searched.sdf │ │ ├── vanilla_core.png │ │ ├── vanilla_core.sdf │ │ └── visualize.ipynb │ ├── makefastfp.py │ ├── query.ipynb │ ├── search_all.py │ ├── search_similarity.py │ ├── search_substructure.py │ └── searchfastfp.py │ └── rdkit_blog │ ├── 2d_edit │ ├── amide.png │ ├── amide2amine.png │ └── amine.png │ ├── 3d_edit │ ├── 5n2d_frag.sdf │ ├── 5n2d_gen.sdf │ ├── editmol_3d.py │ ├── filter.png │ ├── filter_widx.png │ ├── filtered_mol.sdf │ ├── frag_widx.png │ └── gen_widx.png │ ├── 4fny_1.pdb │ ├── 4fny_1_ligand.mol2 │ ├── 5u98_D_rec_5u98_1kx_lig_tt_min_0.sdf │ ├── README.md │ ├── align.sdf │ ├── align_cdk2.sdf │ ├── before_align_cdk2.sdf │ ├── cananicol.ipynb │ ├── clean.ipynb │ ├── generate_confs.py │ ├── geometry │ ├── 1a2g_A_rec.pdb │ ├── 1a2g_A_rec_4jmv_1ly_lig_tt_min_0.sdf │ ├── compute_angle.py │ ├── geometry_neighbor.ipynb │ ├── pdb_parser.py │ └── steric_clash.py │ ├── grid_repre │ ├── grid.png │ ├── grid_computation.py │ ├── htmd2moleculekit.py │ ├── lig.cub │ ├── lig.pdb │ ├── lig.sdf │ ├── lig_occup.npy │ ├── pkt.pdb │ ├── pkt.sdf │ ├── pkt_occup.npy │ └── visualize_grid.py │ ├── highlight_scaffold │ ├── clean.ipynb │ ├── draw_aligned.py │ ├── frag.mol │ ├── output.png │ ├── output2.png │ ├── synthesis_1.mol │ ├── synthesis_2.mol │ ├── synthesis_3.mol │ ├── synthesis_4.mol │ ├── synthesis_5.mol │ ├── synthesis_6.mol │ ├── synthesis_7.mol │ └── synthesis_8.mol │ ├── kekulize_error │ └── kekulize.ipynb │ ├── lead_compound_decomposition │ ├── 1djy_A_rec_1djz_ip2_lig_tt_min_0.sdf │ ├── README.md │ ├── frag.py │ ├── fragmentation.ipynb │ ├── illustration.png │ └── lead_decomp.py │ ├── pocket_UFF.py │ ├── properties_computation │ ├── fragmented.png │ ├── ltk_activates.mol2 │ ├── multi-fused_ring.png │ └── property.py │ ├── qsar │ ├── bindingdb_fgfr3.tsv │ └── process_bindingdb.ipynb │ ├── rdkit.py │ ├── substructure_matching │ ├── aliphatic_core.sdf │ ├── bondtop_core.sdf │ ├── full_mol.jpg │ ├── generic_core_example.png │ ├── generic_partial_mol.jpg │ ├── partial_mol.jpg │ ├── sim_searched.sdf │ ├── utils.py │ ├── vanilla_core.sdf │ └── visualize.ipynb │ ├── torsion.py │ ├── xtb_ecloud │ ├── ori_lig_protein.py │ ├── rotated_lig.cube │ ├── rotated_lig.pdb │ ├── rotated_pkt.cub │ ├── rotated_pkt.pdb │ ├── smiles2ecloud.ipynb │ ├── test.ipynb │ └── xtb_density.py │ └── xyz2mol.py ├── buddha.jpg ├── deep_learning ├── 2022_recommend ├── Self-Teaching ├── gnn.py ├── hard_case_torch_cuda_env │ └── README.md ├── log.txt └── loss_analysis.ipynb ├── figure_making ├── 3D ├── README.md ├── astronomy.png ├── diffusion.png ├── fancy-ideas │ ├── 0c1400278e8068ef61c55168ff49244.jpg │ ├── 1700121861284.png │ ├── 1700121879903.png │ ├── 1700121893932.png │ ├── 3DCNN.png │ ├── 41467_2024_45566_Fig3_HTML.png │ ├── 41570_2018_66_Fig5_HTML.webp │ ├── 41573_2022_542_Fig5_HTML.png │ ├── 41587_2023_2029_Figa_HTML.webp │ ├── 41589_2022_1233_Fig1_HTML.webp │ ├── 42256_2020_174_Fig5_HTML.webp │ ├── 649070a0967bdf5da028ac39_blog_2022-11_protein structure prediction models@1300w.png │ ├── AIDD.jpeg │ ├── AIDD.jpg │ ├── AI_in_multiple_objective_optimization.jpg │ ├── AutoEncoder.png │ ├── CNN-GNN-fusion.jpeg │ ├── Cadd.webp │ ├── DALL·E 2023-11-24 15.35.34 - 炉香乍热。法界蒙薰。诸佛海会悉遥闻。（digital art).png │ ├── DALL·E 2023-11-24 15.35.55 - 一切有为法，如梦幻泡影，如露亦如电，应作如是观。（digital art).png │ ├── DEL_pareto_front.gif │ ├── Deep reinforcement learning in chemistry A review.png │ ├── EGAT.png │ ├── Featured-Blog-Image-A-Comprehensive-Overview-of-Large-Language-Models.jpg │ ├── FragVAE.gif │ ├── GNN-fusion.jpeg │ ├── GNN_illustration.png │ ├── GenAI_protocol.jpg │ ├── LazySlides.png │ ├── MMP_prediction.jpeg │ ├── MOMO_latent_space_GA.jpeg │ ├── MOMO_pareto_vs_scalarization.jpeg │ ├── MoleculeACE.jpeg │ ├── NA.png │ ├── NA_frame.png │ ├── PDBBind_split.png │ ├── PIDiff.png │ ├── README.md │ ├── RNA_backbone.png │ ├── RNA_structures.jpg │ ├── Spectral_attention_networks_!.png │ ├── Spectral_attention_networks_2.png │ ├── active_learning_hte.png │ ├── algorithm-achieves-breakthrough-in-novel-protein-design-365744-1280x720.webp │ ├── chemical_robert.png │ ├── deep_evidential_regression.png │ ├── deep_learning_vaccine_hallucination_11.jpg │ ├── denovo_molecular_design_with_generative_long_short_term_memory.png │ ├── different_Gen_Model.jpg │ ├── different_tasks.png │ ├── docking_and_linking.jpeg │ ├── frag_gold.png │ ├── higher-order-low-order.png │ ├── hotspots.jpeg │ ├── hotspots2.jpeg │ ├── ishida-2019-prediction-and-interpretable.jpeg │ ├── large-language-models.png │ ├── latent space.png │ ├── latent-space.jpeg │ ├── linearizes-the-decision-boundaries-around-a-data-point-to.ppm │ ├── mol_repre.png │ ├── multi-fidelity.webp │ ├── multi_model.jpg │ ├── pharmacophore.png │ ├── pignet.png │ ├── potential_valley.jpg │ ├── pretrained_architecture.png │ ├── protein_survey.png │ ├── representation.jpg │ ├── rfpeptide.png │ ├── rfpeptide_MCL1.png │ ├── sde_models_diffusion.webp │ ├── sequential_docking.jpeg │ ├── sequential_docking_2.jpeg │ ├── similarity_map.png │ ├── test.png │ ├── transformer.png │ ├── virtual_screening.png │ ├── voxel_protein_ligand_hac_net.png │ └── wet-exp-mmp-uncertainty.gif ├── hisplot.png ├── hist.png ├── histplot_box.png ├── join_scatter.png ├── joint_hex.png ├── 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