Add checkpoints: VenusX_Res_BindI_MP90/**

#19
VenusX_Res_BindI_MP90/ankh-large/lr5e-4_bt12k_ga8.json ADDED
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VenusX_Res_BindI_MP90/ankh-large/lr5e-4_bt12k_ga8.pt ADDED
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VenusX_Res_BindI_MP90/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.json ADDED
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VenusX_Res_BindI_MP90/esm2_t33_650M_UR50D/lr5e-4_bt12k_ga8.pt ADDED
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VenusX_Res_BindI_MP90/prot_t5_xl_uniref50/lr5e-4_bt12k_ga8.json ADDED
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