Welcome to PPI Integration Toolkit’s documentation!

Table of Contents

• Backbone Models
  • deepfold
    • deepfold.common
      • deepfold.common.protein
      • deepfold.common.residue_constants
    • deepfold.config
    • deepfold.data
      • deepfold.data.errors
      • deepfold.data.modules
        • deepfold.data.modules.dataloaders
        • deepfold.data.modules.mmcif_dataset
        • deepfold.data.modules.samplers
        • deepfold.data.modules.single_dataset
      • deepfold.data.monomer
      • deepfold.data.multimer
        • deepfold.data.multimer.input_features
        • deepfold.data.multimer.msa_pairing
      • deepfold.data.pdbio
      • deepfold.data.pdbx_parsing
      • deepfold.data.search
        • deepfold.data.search.crfalign
        • deepfold.data.search.input_features
        • deepfold.data.search.mmcif
        • deepfold.data.search.msa_identifiers
        • deepfold.data.search.parsers
        • deepfold.data.search.templates
      • deepfold.data.tools
        • deepfold.data.tools.hhblits
        • deepfold.data.tools.hhsearch
        • deepfold.data.tools.hmmbuild
        • deepfold.data.tools.hmmsearch
        • deepfold.data.tools.jackhmmer
        • deepfold.data.tools.kalign
        • deepfold.data.tools.utils
    • deepfold.distributed
      • deepfold.distributed.model_parallel
      • deepfold.distributed.utils
    • deepfold.eval
      • deepfold.eval.cell_lists
      • deepfold.eval.contact
      • deepfold.eval.distogram
      • deepfold.eval.msa
      • deepfold.eval.plot
      • deepfold.eval.pseudo_3d
    • deepfold.loss
    • deepfold.losses
      • deepfold.losses.auxillary
      • deepfold.losses.confidence
      • deepfold.losses.geometry
      • deepfold.losses.masked_msa
      • deepfold.losses.procrustes
      • deepfold.losses.utils
      • deepfold.losses.violation
    • deepfold.modules
      • deepfold.modules.alphafold
      • deepfold.modules.angle_resnet
      • deepfold.modules.attention
      • deepfold.modules.auxiliary_heads
      • deepfold.modules.backbone_update
      • deepfold.modules.dropout
      • deepfold.modules.evoformer_block
      • deepfold.modules.evoformer_block_pair_core
      • deepfold.modules.evoformer_stack
      • deepfold.modules.extra_msa_block
      • deepfold.modules.extra_msa_embedder
      • deepfold.modules.extra_msa_stack
      • deepfold.modules.global_attention
      • deepfold.modules.inductor
      • deepfold.modules.input_embedder
      • deepfold.modules.invariant_point_attention
      • deepfold.modules.layer_norm
      • deepfold.modules.linear
      • deepfold.modules.msa_column_attention
      • deepfold.modules.msa_column_global_attention
      • deepfold.modules.msa_row_attention_with_pair_bias
      • deepfold.modules.msa_transition
      • deepfold.modules.outer_product_mean
      • deepfold.modules.pair_transition
      • deepfold.modules.recycling_embedder
      • deepfold.modules.single_transition
      • deepfold.modules.structure_module
      • deepfold.modules.template_angle_embedder
      • deepfold.modules.template_pair_block
      • deepfold.modules.template_pair_embedder
      • deepfold.modules.template_pair_stack
      • deepfold.modules.template_pointwise_attention
      • deepfold.modules.template_projection
      • deepfold.modules.triangular_attention
      • deepfold.modules.triangular_multiplicative_update
      • deepfold.modules.tweaks
        • deepfold.modules.tweaks.evo_attn
    • deepfold.ops
      • deepfold.ops.evoformer_attention
    • deepfold.package_info
    • deepfold.relax
      • deepfold.relax.amber_minimize
      • deepfold.relax.cleanup
      • deepfold.relax.relax
      • deepfold.relax.utils
    • deepfold.runner
      • deepfold.runner.config_utils
      • deepfold.runner.parser
      • deepfold.runner.utils
    • deepfold.testing
      • deepfold.testing.common
      • deepfold.testing.utils
    • deepfold.train
      • deepfold.train.gradient_clipping
      • deepfold.train.lr_scheduler
      • deepfold.train.validation_metrics
    • deepfold.utils
      • deepfold.utils.checkpoint_utils
      • deepfold.utils.chunk_utils
      • deepfold.utils.crop_utils
      • deepfold.utils.datetime_utils
      • deepfold.utils.dist_utils
      • deepfold.utils.feats_utils
      • deepfold.utils.file_utils
      • deepfold.utils.geometry
        • deepfold.utils.geometry.quat_rigid
        • deepfold.utils.geometry.rigid_matrix_vector
        • deepfold.utils.geometry.rotation_matrix
        • deepfold.utils.geometry.utils
        • deepfold.utils.geometry.vector
      • deepfold.utils.hash_utils
      • deepfold.utils.import_utils
      • deepfold.utils.iter_utils
      • deepfold.utils.log_utils
      • deepfold.utils.precision
      • deepfold.utils.random
      • deepfold.utils.rigid_utils
      • deepfold.utils.script_utils
      • deepfold.utils.swa_utils
      • deepfold.utils.tensor_utils
  • miniworld
    • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
    • miniworld.feature
      • miniworld.feature.MiniWorld_featuring_species
    • miniworld.models_MiniWorld_v1_5_use_interaction
      • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module
      • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor
      • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings
      • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld
      • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module
      • miniworld.models_MiniWorld_v1_5_use_interaction.value_network
    • miniworld.utils
      • miniworld.utils.DataClass
      • miniworld.utils.My_mistake
      • miniworld.utils.ProteinClass
      • miniworld.utils.arguments_MiniWorld
      • miniworld.utils.chemical
      • miniworld.utils.data_refactoring
      • miniworld.utils.ffindex
      • miniworld.utils.hhpred_parser
      • miniworld.utils.kalign_mapping
      • miniworld.utils.kinematics
      • miniworld.utils.output_visualize
      • miniworld.utils.parser_util
      • miniworld.utils.template_parser
      • miniworld.utils.util
      • miniworld.utils.util_module
• Tools
  • bapred
    • bapred.data
      • bapred.data.atom_feature
      • bapred.data.data
      • bapred.data.utils
    • bapred.inference
    • bapred.model
      • bapred.model.GatedGCNLSPE
      • bapred.model.GraphGPS
      • bapred.model.MHA
      • bapred.model.model
  • bindingrmsd
    • bindingrmsd.data
      • bindingrmsd.data.data
      • bindingrmsd.data.data_bck
      • bindingrmsd.data.ligand_atom_feature
      • bindingrmsd.data.protein_atom_feature
      • bindingrmsd.data.utils
    • bindingrmsd.inference
    • bindingrmsd.model
      • bindingrmsd.model.GatedGCNLSPE
      • bindingrmsd.model.model
  • bis_protein_structure
    • bis_protein_structure.CROSSLINK
    • bis_protein_structure.DATAGEN
    • bis_protein_structure.DISULFIDE
    • bis_protein_structure.MMEVAL
    • bis_protein_structure.SOLVENTACC
    • bis_protein_structure.TORSION2
    • bis_protein_structure.residue_constants
    • bis_protein_structure.split_pdb
  • bsitep
    • bsitep.proteindata
    • bsitep.seresnet
    • bsitep.utils
      • bsitep.utils.data_utils
      • bsitep.utils.model_utils
      • bsitep.utils.pocket_utils
  • diffalign
    • diffalign.models
      • diffalign.models.common
      • diffalign.models.encoder
        • diffalign.models.encoder.edge
        • diffalign.models.encoder.egnn
      • diffalign.models.epsnet
        • diffalign.models.epsnet.diffusion
    • diffalign.train
    • diffalign.utils
      • diffalign.utils.chem
      • diffalign.utils.common
      • diffalign.utils.dataloader
      • diffalign.utils.datasets
      • diffalign.utils.evaluation
        • diffalign.utils.evaluation.covmat
      • diffalign.utils.misc
      • diffalign.utils.transforms
      • diffalign.utils.visualize
  • gd_dl
    • gd_dl.data
      • gd_dl.data.ML_inference
      • gd_dl.data.ML_rerank
      • gd_dl.data.all_ML_rerank
      • gd_dl.data.single_ML_rerank
    • gd_dl.lib_pdb_mol2
    • gd_dl.models
    • gd_dl.path_setting
    • gd_dl.rerank_model
    • gd_dl.utils
  • promptbind
    • promptbind.data
      • promptbind.data.data
      • promptbind.data.inference_preprocess_mol_confs
      • promptbind.data.inference_preprocess_protein
    • promptbind.models
      • promptbind.models.att_model
      • promptbind.models.cross_att
      • promptbind.models.egnn
      • promptbind.models.model
      • promptbind.models.model_utils
    • promptbind.test_promptbind
    • promptbind.train_promptbind
    • promptbind.utils
      • promptbind.utils.fabind_inference_dataset
      • promptbind.utils.feature_utils
      • promptbind.utils.generation_utils
      • promptbind.utils.inference_mol_utils
      • promptbind.utils.inference_pdb_utils
      • promptbind.utils.logging_utils
      • promptbind.utils.metrics
      • promptbind.utils.metrics_to_tsb
      • promptbind.utils.post_optim_utils
      • promptbind.utils.utils
    • promptbind.visualize_prompt_components
• Examples
  • EGFR-antibody interaction analysis
    • Section 2: Finding binding pockets for EGFR KD using “BsiteP”
      • #Section 3: Conducting Protein-Ligand Complex Structure Prediction Using GDDL
  • EGFR-ligand interaction analysis
    • Tips and Instructions
  • EGFR-ligand interaction analysis
    • Section 2: Finding binding pockets for a given protein (EGFR) using “BsiteP”
      • ## Benchmarking results of binding site prediction method
      • #Section 3: Conducting Protein-ligand Docking Using GDDL
    • Section 4: Re-scoring GDDL docking results using BindingRMSD.
    • 4-1. Re-scoring for Docked Protein-Ligand Complex
    • 4-2. 3D Visualization: Crystal Structure vs Docked Poses
    • 4-3. Crystal Ligand Pose vs Docked Ligand Pose: RMSD and Prediction Comparison

Indices and tables

• Index

• Module Index

• Search Page