Commit 9320b710 authored by Studer Gabriel's avatar Studer Gabriel
Browse files

modelling: fetch target structures and target sequences from CAMEO

parent 54bc72eb
Scripts and data to reproduce the homology modelling accuracy benchmark.
The whole benchmark is a three step process:
1. Benchmark generation
2. Modelling with ProMod3 and MODELLER
3. Evaluation
1. Benchmark generation
First you need to download raw modeling evaluation data from cameo3d.org.
However, for the template selection you need access to a SWISS-MODEL instance
registered to CAMEO. We document the steps we performed but suggest to skip this
step and stick to the data we provide to you.
- download raw modelling evaluation data from CAMEO. Data for the last three
months is available here: https://www.cameo3d.org/sp/3-months/
- adapt the **eval_dir**, **start_date** and **end_date** variables in
fetch_cameo_targets.py and run the script.
>2020-05-30_00000001_1
MTITALPTGLYAEVLSFYGHQMQKLDGRDFAGYAATFTEDGEFRHSPSLPAAHTRAGITAVLEDFHRKFDARKIQRRHWFDHTALSQASDGSITATSYCLVLTVHADVKAPEFGPSCLVHDVLVRGADGELLLRSRHVTHDHVFPA
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>2020-05-02_00000000_1
MATANVAGAGGSGSEPTRIAILGKEDIIVDHGIWLNFVAHDLLQTLPSSTYVLITDTNLYTTYVPPFQAVFEAAAPRDVRLLTYAIPPGEYSKSRETKAEIEDWMLSHACTRDTVIIALGGGVIGDMIGYVAATFMRGVRFVQVPTTLLAMVDSSIGGKTAIDTPMGKNLIGAFWQPRRIYIDLAFLETLPVREFINGMAEVIKTAAIWNETEFTALEENAAAILEAVRSKASSPAARLAPIRHILKRIVLGSARVKAEVVSADEREGGLRNLLNFGHSIGHAYEAILAPQVLHGECVAIGMVKEAELARYLGVLRPSAVARLTKLIASYDLPTSVHDKRIAKLSAGKECPVDVLLQKMAVDKKNEGRKKKIVLLSAIGKTYEKKATVVDDRAIRLVLSPSVRVTPGVPKGLSVTVTPPGSKSISNRALVLAALGEGTTRIHGLLHSDDVQYMLAAIEQLHGADFSWEDAGEILVVTGKGGKLQASKEPLYLGNAGTASRFLTSVVALCAPSAVSSTVLTGNARMKVRPIGALVDALRANGVGVKYLEKEKSLPVEVDAAGGFAGGVIELAATVSSQYVSSILMAAPYAHQPVTLRLVGGKPISQPYIDMTIAMMASFGIKVERSAEDPNTYLIPKGVYKNPPEYVVESDASSATYPLAVAAITGTTCTIPNIGSESLQGDARFAVEVLRPMGCAVEQTATSTTVTGPPIGTLKAIPHVDMEPMTDAFLTAAVLAAVADGTTQITGIANQRVKECNRIAAMKDQLAKFGVQCNELEDGIEVIGKPYQELRNPVEGIYCYDDHRVAMSHSVLSTISPHPVLILERECTAKTWPGWWDILSQFFKVQLDGEEDPTKRTTQSTQQVRKGTDRSIFIVGMRGAGKSTAGRWMSELLKRPLVDLDAELERREGMTIPEIIRGERGWEGFRQAELELLQDVIKNQSKGYIFSCGGGIVETEAARKLLIDYHKNGGPVLLVHRDTDQVVEYLMRDKTRPAYSENIREVYERRKPWFYECSNLQYHSPHEDGSEALLQPPADFARFVKLIAGQSTHLEDVRAKKHSFFVSLTVPNVADALDIIPRVVVGSDAVELRVDLLESYEPEFVARQVALLRAAAQVPIVYTVRTQSQGGKFPDEDYDLALRLYQTGLRSGVEYLDLEMTMPDHILQAVTDAKGFTSIIASHHDPQCKLSWKSGSWIPFYNKALQYGDVIKLVGVAREMADNFALTNFKAKMLAAHDNKPMIALNMGTAGKLSRVLNGFLTPVSHPALPSKAAPGQLSATEIRQALSLIGEIEPKSFYLFGKPISASRSPALHNTLFYKTGLPHHYSRFETDEASKALESLIRSPDFGGASVTIPLKLDIMPLLDSATDAARTIGAVNTIIPQTRDGSTTTLVGDNTDWRGMVHALLHSSGSGSVVQRTAAPRGAAMVVGSGGTARAAIYALHDLGFAPIWIVARSEERVAELVRGFDGYDLRRMTSPHQGKDNMPSVVISTIPATQPIDPSMREVIVEVLKHGHPSAEGKVLLEMAYQPPRTPLMTLAEDQGWRTVGGLEVLAAQGWYQFQLWTGITPLYEEARAAVMGEDSVELEHHHHHH
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>2020-04-25_00000038_1
GSMDQPAGLQVDYVFRGVEHAVRVMVSGQVLELEVEDRMTADQWRGEFDAGFIEDLTHKTGNFKQFNIFCHMLESALTQSSESVTLDLLTYTDLESLRNRKMGGRPGSLAPRSAQLNSKRYLILIYSVEFDRIHYPLPLPYQGKP
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>2020-03-28_00000015_1
GMPPPADIVKVAIEWPGAYPKLMEIDQKKPLSAIIKEVCDGWSLANHEYFALQHADSSNFYITEKNRNEIKNGTILRLTTSPAQNAQQLHERIQSSSMDAKLEALKDLASLSRD
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>2020-03-28_00000021_1
GSMRGKVSLEEAFELPKFAAQTKEKAELYIAPNNRDRYFEEILNPCGNRLELSNKHGIGYTIYSIYSPGPQGWTERAECEEYARECNDYISGEIANHKDRMGAFAALSMHDPKQASEELTRCVKELGFLGALVNDVQHAGPEGETHIFYDQPEWDIFWQTCVDLDVPFYLHPEPPFGSYLRNQYEGRKYLIGPPVSFANGVSLHVLGMIVNGVFDRFPKLKVILGHLGEHIPGDFWRIEHWFEHCSRPLAKSRGDVFAEKPLLHYFRNNIWLTTSGNFSTETLKFCVEHVGAERILFSVDSPYEHIDVGCGWYDDNAKAIMEAVGGEKAYKDIGRDNAKKLFKLGKFYDSEA
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>2020-04-04_00000026_1
TMTSVGVRALRQQASELLRRVEAGETIEITDRGRPVALLSPLPQ
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>2020-05-02_00000006_1
DVQLVESGGGLVQAGGSLRLSCTASGFTFDDYTMGWFRQAPGKEREGVSYTGWSGSMSGSTTYYTDSVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAARYRGIGSQVRWTDFIYWGQGTQVTVSS
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>2020-05-09_00000013_1
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMTVPHIPRGPVMADIAAFRLTEEEKQRLLDPAIGGIILFRRNFQNIEQLKTLTAEIKALRTPELIIAVDHEGGRVQRFIEGFTRLPAMNVLGQIWDKDGASAAETAAGQVGRVLATELSACGIDLSFTPVLDLDWGNCAVIGNRSFHRNPEAVARLALALQKGLAKGGMKSCGKHFPGHGFVEGDSHLVLPEDGRSLDELEAADLAPFRIMSREGMAAVMPAHVVYPQVDTKPAGFSEIWLKQILRRDIGFKGVIFSDDLTMEGACGAGGIKERARISFEAGCDIVLVCNRPDLVDELRDGFTIPDNQDLAGRWQYMENSLGHEAVQAVMQTMGFQAAQAFVAGLASPQDTAGGVKVGEAF
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>2020-04-18_00000087_1
DLQLLHQKVEEQAAKYKHRVPKKCCYDGARENKYETCEQRVARVTIGPHCIRAFNECCTIADKIRKNISHKFAPAAR
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>2020-04-18_00000087_2
DLQLLHQKVEEQAAKYKHRVPKKCCYDGARENKYETCEQRVARVTIGPHCIRAFNECCTIADKIRKESHHKGMLLGR
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