{
"repository": "https://github.com/dauparas/ProteinMPNN",
"commit": "8907e6671bfbfc92303b5f79c4b5e6ce47cdef57",
"input_reference": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/README.md",
"implementation_reference": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/protein_mpnn_run.py",
"assets": [
{
"path": "inputs/PDB_complexes/pdbs/3HTN.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_complexes/pdbs/3HTN.pdb",
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{
"path": "inputs/PDB_complexes/pdbs/4YOW.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_complexes/pdbs/4YOW.pdb",
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{
"path": "inputs/PDB_homooligomers/pdbs/4GYT.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_homooligomers/pdbs/4GYT.pdb",
"sha256": "4a5e02d9235d13af82854d7f0e4ca72e00c58351a30645575a104064dc1ff1a2"
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{
"path": "inputs/PDB_homooligomers/pdbs/6EHB.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_homooligomers/pdbs/6EHB.pdb",
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{
"path": "inputs/PDB_monomers/pdbs/5L33.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_monomers/pdbs/5L33.pdb",
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{
"path": "inputs/PDB_monomers/pdbs/6MRR.pdb",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PDB_monomers/pdbs/6MRR.pdb",
"sha256": "310906dfdf1c0e5ada9ea8dad600a992bd83a8d53233fd5b034a556702aff9a2"
},
{
"path": "LICENSE",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/LICENSE",
"sha256": "82009d25ce585631f452b2b24589bdb29c559ccfefa2f200ef312ed5b501a586"
},
{
"path": "outputs/example_3_outputs/seqs/3HTN.fa",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/outputs/example_3_outputs/seqs/3HTN.fa",
"sha256": "32be7f7b15736faeea140b473e2eb99d6b92cdfc3554ac526bcd2750cc55d23a"
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{
"path": "inputs/PSSM_inputs/3HTN.json",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PSSM_inputs/3HTN.npz",
"source_sha256": "0f93dfdf6da0336cbe6a0d09fb6c7d31670f73afb3157a7d43b76c032c89f4c6",
"sha256": "1e5de41e6bb8a9d80463fca2f7ebc7978fcbd4a1de12d05290e6ee29412df486",
"conversion": "NumPy arrays converted to the chain dictionary used by helper_scripts/make_pssm_input_dict.py; numeric values preserved."
},
{
"path": "inputs/PSSM_inputs/4YOW.json",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/inputs/PSSM_inputs/4YOW.npz",
"source_sha256": "8b26254422205d1751ccae4ee02f120a6320f756185637685160f061739039d5",
"sha256": "b3c83e64a29630484a4389e625e8037daaddc824dcdef8c4d839582f278e5bad",
"conversion": "NumPy arrays converted to the chain dictionary used by helper_scripts/make_pssm_input_dict.py; numeric values preserved."
}
],
"adaptations": [
"Folder-based examples are split into one preset per PDB. The service supplies the PDB directly and creates target-keyed constraint files in each job directory.",
"The FASTA scoring example\u2019s author-specific absolute path is replaced with the bundled outputs/example_3_outputs/seqs/3HTN.fa from the same upstream commit.",
"The non-fixed example is represented by the fixed-position complement generated from each parsed chain length.",
"PSSM NPZ arrays are bundled as text JSON with the same numeric values and chain keys as the official helper output.",
"The task selector maps to score_only, conditional_probs_only and unconditional_probs_only; design leaves these flags disabled.",
"pdb_path, path_to_fasta and JSON/JSONL fields accept uploaded contents or catalog assets, not server filesystem paths. Output directories, model paths, jsonl_path and chain_id_jsonl are managed by the single-structure adapter.",
"The installed soluble_model_weights directory contains 002, 010, 020 and 030 despite the README\u2019s shorter list. CA-only supports 002, 010 and 020; CA-soluble weights are unavailable."
],
"validation": {
"date": "2026-09-05",
"runtime": "Python 3.12, PyTorch 2.7.1 CPU, NumPy 1.26.4",
"official_examples": 21,
"checks": [
"All 21 bundled presets completed actual CPU inference, including FASTA scoring, fixed/tied positions, homooligomers, unconditional probabilities and PSSM guidance.",
"Verified output sequence counts and finite numeric score/probability outputs.",
"Also exercised conditional backbone-only probabilities.",
"All presets passed browser form submission and official argument-parser checks.",
"Verified wrapped mmCIF rows and first-model selection.",
"Representative adapter calls passed the actual bio_tools subprocess runner and durable result archiving."
],
"limits": "CUDA and Ubuntu deployment were not exercised on this Windows host."
}
}