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Added BFVD as a foldseek database #344

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merged 6 commits into from
Sep 10, 2024
Merged

Added BFVD as a foldseek database #344

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6c733a5
Added BFVD as structure database
rachelse Sep 6, 2024
9593d05
Minor modification
rachelse Sep 6, 2024
de698ca
Added version file
rachelse Sep 6, 2024
31707e9
Distinguished BFMD and BFVD
rachelse Sep 6, 2024
8e146c2
Changed url to the db
rachelse Sep 6, 2024
ff8753a
Add biorxiv id, enable taxdb flag and reorder
milot-mirdita Sep 10, 2024
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8 changes: 8 additions & 0 deletions data/structdatabases.sh
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Expand Up @@ -182,6 +182,14 @@ case "${SELECTION}" in
tar xvfz "${TMP_PATH}/${MODEL}" -C "${OUTDB}"
INPUT_TYPE="MODEL_WEIGHTS"
;;
"BFVD")
if notExists "${TMP_PATH}/bfvd.tar.gz"; then
downloadFile "https://bfvd.steineggerlab.workers.dev/bfvd_foldseekdb.tar.gz" "${TMP_PATH}/bfvd.tar.gz"
downloadFile "https://bfvd.steineggerlab.workers.dev/bfvd.version" "${TMP_PATH}/version"
fi
tar xvfz "${TMP_PATH}/bfvd.tar.gz" -C "${TMP_PATH}"
push_back "${TMP_PATH}/bfvd"
INPUT_TYPE="FOLDSEEK_DB"
esac

if notExists "${OUTDB}.dbtype"; then
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10 changes: 9 additions & 1 deletion src/FoldseekBase.cpp
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Expand Up @@ -435,11 +435,19 @@ std::vector<DatabaseDownload> externalDownloads = {
{
"BFMD",
"BFMD Big fantastic multimer database (combined multimers from large prediction projects).",
"Kim et al. Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer. bioRxiv (2024)",
"Kim W et al. Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer. bioRxiv (2024)",
"https://foldseek.steineggerlab.workers.dev/bfmd.version",
true, Parameters::DBTYPE_AMINO_ACIDS, structdatabases_sh, structdatabases_sh_len,
{}
},
{
"BFVD",
"BFVD Big fantastic virus database (predicted viral protein structures based on the viral sequence representatives of the UniRef30 clusters",
"Kim R et al. BFVD - a large repository of predicted viral protein structures. bioRxiv, 2024.09.08.611582v1 (2024)",
"https://bfvd.steineggerlab.workers.dev",
true, Parameters::DBTYPE_AMINO_ACIDS, structdatabases_sh, structdatabases_sh_len,
{}
},
{
"ProstT5",
"Protein language model to predict 3Di directly from sequence.",
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