{
 "tool": "prostt5",
 "name": "ProstT5 + Foldseek",
 "kind": "compares 3-D shape letters (3Di)",
 "compares": "Shape letters (3Di) predicted from the amino-acid sequence by the ProstT5 protein language model, then searched with Foldseek, so no AlphaFold model is needed.",
 "needs": {
  "sequence only": true,
  "3D structure prediction": false,
  "GPU": true
 },
 "reference": "3Di letters predicted by ProstT5 for the relative's proteome (Quest for Orthologs reference proteomes, release 2020_04), as a Foldseek database.",
 "score": "Bit score: higher ranks first. The E-value cutoff was 10.",
 "failure_modes": [
  "Proteins longer than 6,000 residues are skipped before the 3Di letters are predicted, and are listed in a skipped-proteins file.",
  "Predicting the 3Di letters ran on one GPU (foldseek createdb --gpu 1). For the 998 queries that step is counted in the GPU column and the cost; for each relative's proteome it is a one-off database build and is not counted."
 ],
 "version": "Foldseek 10.941cd33 with ProstT5 weights",
 "licence": "GPL-3.0 (Foldseek); MIT (ProstT5 model weights)",
 "commercial_use": "Yes. Foldseek's GPL-3.0 applies to changed versions you distribute.",
 "licence_url": "https://huggingface.co/Rostlab/ProstT5",
 "container": "quay.io/biocontainers/foldseek:10.941cd33--h5021889_1 (sha256:1156a052f31b2afb85257c02e83a962f559c9752273fe1064ab735f90ac29d1a)",
 "command": "foldseek createdb filtered.fasta zebrafish_prostt5/db \\\n    --prostt5-model weights --gpu 1 --threads 8\n\nfoldseek search \\\n    human-38fdd87d_prostt5/db zebrafish_prostt5/db result tmp \\\n    --threads 16 \\\n    -e 10.0 \\\n    --max-seqs 1000",
 "numbers_from": {
  "repo": "seanome/2024-kmerseek-analysis",
  "commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
  "filters": "pfam, raw, zebrafish"
 },
 "best_setting": "3di_from_seq",
 "strong": [
  {
   "axis": "identity",
   "stratum": "no_homolog",
   "fmax": 0.019770817207544145,
   "n": 321,
   "other_tool": "hhblits",
   "other_setting": "single_seq",
   "other_fmax": 0.03236195478661682,
   "margin": -0.012591137579072674
  },
  {
   "axis": "identity",
   "stratum": "30-40%",
   "fmax": 0.14395007502778603,
   "n": 165,
   "other_tool": "mmseqs2_iterative",
   "other_setting": "s7",
   "other_fmax": 0.20886402027992682,
   "margin": -0.06491394525214078
  }
 ],
 "weak": [
  {
   "axis": "feature_length_bin",
   "stratum": "16-30",
   "fmax": 0.0001885191818267509,
   "n": 271,
   "other_tool": "kmerseek",
   "other_setting": "wwmj5_k11_lcFalse",
   "other_fmax": 0.3297506857792661,
   "margin": -0.3295621665974393
  },
  {
   "axis": "feature_length_bin",
   "stratum": "31-60",
   "fmax": 0.03167736406589417,
   "n": 420,
   "other_tool": "kmerseek",
   "other_setting": "gbmr4_k21_lcFalse",
   "other_fmax": 0.23209537155652643,
   "margin": -0.20041800749063227
  }
 ],
 "cost_per_1000_queries": {
  "core_h_reserved_per_relative": 0.10895865805685447,
  "n_relatives": 15,
  "database_build_core_h": 5.3133333333333335,
  "database_build_gpu_h": 0.6641666666666667,
  "peak_rss_gb": 1.5,
  "hardware": "Stanford Sherlock, SLURM partition hns"
 },
 "questions": [
  "Is the closest same-family domain in the relative you will search at least 40% identical, for most of your proteins? If yes, Fmax here is 40\u201360% 0.139 (n = 563), 60\u2013100% 0.209 (n = 1,289). If no, 20\u201330% 0.247 (n = 93), 30\u201340% 0.144 (n = 165). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting shape letters from sequence; subsets with at least 30 true instances.)",
  "Do you have a GPU to predict the 3Di letters for your proteins? The run used one GPU for that step; its cost is not counted here.",
  "Can you spend about 0.109 core-hours per 1,000 proteins for each relative you search? That is the measured mean per relative; see \"Cost per 1,000 queries\" below."
 ],
 "markdown": "prostt5.md"
}