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Supplementary Table 4. The statistical information of the additional benchmark
datasets. To evaluate the performance of binary interaction prediction task, we also
generated the negative samples using the same strategy as described in the Methods
section (i.e., shuffling the non-interacting pairs). All these datasets were essentially
derived from the Protein Data Bank (PDB). \Num" is the abbreviation of \Number".
The text was updated successfully, but these errors were encountered:
dlemas
changed the title
CAMP: Proteins Reported in Manuscript
Supplementary Note 5: Additional results on Generalizability on additional benchmark datasets
Sep 26, 2022
dlemas
changed the title
Supplementary Note 5: Additional results on Generalizability on additional benchmark datasets
BENCHMARK DATA: PPDbench
Oct 13, 2022
Update on ppdbench. the files have been distributed to the team. we will start with the ligand files (133). There is a file called ./ppdbench_metadata.csv with all the file names for ligand pdb files.
Next steps to create the PLIP files for benchmark data includes:
read the file: ./ppdbench_metadata.csv. this file contains all "ligand" pdb files.
read the directory with ligand pdb files
load biopython
read each pdb file and output the sequence as a column in ./ppdbench_metadata.csv
How do I get the sequence of a structure?
The first thing to do is to extract all polypeptides from the structure (see previous entry). The sequence of each polypeptide can then easily be obtained from the Polypeptide objects. The sequence is represented as a Biopython Seq object.
Supplementary Table 4. The statistical information of the additional benchmark
datasets. To evaluate the performance of binary interaction prediction task, we also
generated the negative samples using the same strategy as described in the Methods
section (i.e., shuffling the non-interacting pairs). All these datasets were essentially
derived from the Protein Data Bank (PDB). \Num" is the abbreviation of \Number".
The text was updated successfully, but these errors were encountered: