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Plip #11

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Plip #11

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ebb0c38
remove old data files
dlemas Oct 12, 2022
e79754b
add PPDbench files
dlemas Oct 12, 2022
26d3c52
ppdbench update
dlemas Oct 12, 2022
cc765d5
update pdb_metadata
dlemas Oct 12, 2022
8a8a9fe
add plip results
dlemas Oct 12, 2022
9035b30
update demo-data
dlemas Oct 12, 2022
919c73f
rename step1_0.py
dlemas Oct 12, 2022
44ca609
rename step1_2.rmd
dlemas Oct 12, 2022
02fcc3b
update step1
dlemas Oct 13, 2022
e2110d7
Create ppdbench_format.txt
dlemas Oct 13, 2022
cc19ef4
remove files that are not required
dlemas Oct 13, 2022
0d5289e
metadata updated w/ sequences
evanhadam Oct 18, 2022
ad4023e
pdb_lookup
evanhadam Oct 18, 2022
afcacb3
rename to pdb_to_sequence
evanhadam Oct 18, 2022
ddff88e
fixed ppdbench_metadata.csv to contain peptide sequences, next step i…
AnthonyYao7 Oct 21, 2022
6f5dd57
Updated to include failed 4dcb. No such 4dcb pdb file
AnthonyYao7 Oct 24, 2022
e7f4d1e
fixed plip file names
AnthonyYao7 Oct 25, 2022
337e47c
fixed merge conflict
AnthonyYao7 Oct 25, 2022
4acfa2d
step 1 fully working
AnthonyYao7 Oct 27, 2022
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1 change: 0 additions & 1 deletion data_prepare/ppdbench_metadata.csv
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6 changes: 5 additions & 1 deletion data_prepare/step1/df_predict_det1
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@@ -1,4 +1,8 @@
pdb_id pep_chain predicted_chain pep_seq prot_seq pep_seq_len prot_seq_len peptide_seq_score
1cjr a b KETAAAKFERQHMDS NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 15 101 1.0
1cvu f a TKTATINAS ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTAQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQ 9 552 1.0
1cka b a PPPALPPKKR AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKY 10 57 1.0
1cvu f b TKTATINAS ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTAQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQ 9 552 1.0
1d4t b a KSLTIYAQVQK MDAVAVYHGKISRETGEKLLLATGLDGSYLLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLISAFQKPDQGIVIPLQYPVEK 11 104 1.0
1eg4 p a KNMTPYRSPPPYVPP GPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAET 15 261 1.0
1h6w b a SLNYIIKVKE LSYPNATESVYGLTRYSTNDEAIAGVNNESSITPAKFTVALNNVFETRVSTESSNGVIKISSLPQALAGADDTTAMTPLKTQQLAVKLIAQIAPSKNAATESEQGVIQLATVAQARQGTLREGYAISPYTFMNSTATEEYKGVIKLGTQSEVNSNNASVAVTGATLNGRGSTTSMRGVVKLTTTAGSQSGGDASSALAWNADVIHQRGGQTINGTLRINNTLTIASGGANITGTVNMTGGYIQGKRVVTQNEIDRTIPVGAIMMWAADSLPSDAWRFCHGGTVSASDCPLYASRIGTRYGGSSSNPGLPDMR 10 312 1.0
1hc9 c a WRYYESSLLPYPD IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG 13 74 1.0
6 changes: 5 additions & 1 deletion data_prepare/step1/df_predict_det3
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Original file line number Diff line number Diff line change
@@ -1,4 +1,8 @@
SP_PRIMARY
P61823
Q64010
Q05769
Q05769
O60880
P11532
P10930
P60616
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