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alphafold2-model-2

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alphafold2-model-2
File size: 2,788 Bytes
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{
  "architecture": "alphafold2",
  "evoformer": {
    "block": {
      "msa_row_attention_with_pair_bias": {
        "dropout": 0.15,
        "num_attention_heads": 8
      },
      "msa_transition": {
        "expansion": 4
      },
      "outer_product_mean": {
        "first": false,
        "hidden_size": 32
      },
      "pair_transition": {
        "expansion": 4
      },
      "triangle_attention_starting_node": {
        "dropout": 0.25,
        "head_size": 32,
        "num_attention_heads": 4
      },
      "triangle_multiplication_outgoing": {
        "hidden_size": 128
      }
    },
    "extra_msa_size": 64,
    "msa_size": 256,
    "num_blocks": 48,
    "num_extra_msa_blocks": 4,
    "pair_size": 128,
    "single_size": 384
  },
  "heads": {
    "distogram": {
      "num_distogram_bins": 64
    },
    "experimentally_resolved": {
      "num_atom_types": 37
    },
    "predicted_aligned_error": {
      "enabled": false,
      "max_error_bin": 31.0,
      "num_pae_bins": 64
    },
    "predicted_lddt": {
      "hidden_size": 128,
      "num_plddt_bins": 50
    }
  },
  "input_embeddings": {
    "max_relative_feature": 32,
    "token_feature_size": 73
  },
  "msa": {
    "gap_agreement_weight": 0.0,
    "masked_msa_enabled": true,
    "masked_msa_profile_prob": 0.1,
    "masked_msa_replace_fraction": 0.15,
    "masked_msa_same_prob": 0.1,
    "masked_msa_uniform_prob": 0.1,
    "max_extra_msa": 1024,
    "max_msa_clusters": 508,
    "msa_cluster_features": true,
    "resample_msa_in_recycling": true
  },
  "num_ensembles": 1,
  "num_recycles": 4,
  "recycling": {
    "previous_positions": {
      "max_distance": 20.75,
      "min_distance": 3.25,
      "num_distogram_bins": 15
    },
    "recycle_features": true,
    "recycle_positions": true
  },
  "structure_module": {
    "dropout": 0.1,
    "hidden_size": 384,
    "num_attention_heads": 12,
    "num_blocks": 8,
    "num_point_qk": 4,
    "num_point_v": 8,
    "num_transition_projections": 3,
    "position_scale": 10.0,
    "scalar_query_key_size": 16,
    "scalar_value_size": 16,
    "sidechain": {
      "hidden_size": 128,
      "num_blocks": 2
    }
  },
  "template": {
    "attention": {
      "num_attention_heads": 4
    },
    "embed_torsion_angles": true,
    "enabled": true,
    "max_distance": 50.75,
    "min_distance": 3.25,
    "num_distogram_bins": 39,
    "template_pair_stack": {
      "num_blocks": 2,
      "pair_size": 64,
      "transition": {
        "expansion": 2
      },
      "triangle_attention_starting_node": {
        "dropout": 0.25,
        "head_size": 16,
        "num_attention_heads": 4
      },
      "triangle_multiplication_outgoing": {
        "hidden_size": 64
      }
    },
    "use_template_unit_vector": false,
    "vocab_size": 22
  }
}