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twopin / CAMP

predicting peptide-protein interactions
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Could you check PLIPv2.2.2 output vs v1.4.2? current codes only for PLIPv1.4.2? #24

Closed rocke2020 closed 2 years ago

rocke2020 commented 2 years ago

Dear twopin,

It is my honor to read your paper and codes, excellent idea to merge so many data and excellent model design. I try to reproduce your work. In data_prepare/step1_pdb_process.py, from your example file, PLIPv1.4.2 is used, current version is v2.2.2. I compare the same PDB 1A0M, the v2.2.2 output is quite different with v1.4.2. Could you update you code with PLIP v2.2.2, or could you give us instructions on how to deal with PLIPv2.2.2? thanks!! From your codes, with PLIPv1.4.2, 1 PDB code may output multiple result files: './peptide_result/' + pdbid + '' + chain + '_result.txt', that's one chain one result file, yes? With PLIPv2.2.2, 1 PDB code ouput only 1 result file with possible multiple Interacting chain. 1A0M-v1.4.2.txt 1A0M-v2.2.2.txt

rocke2020 commented 2 years ago

Solved. Don't use PLIPv2 default mode, but use Detection of Protein-Peptide Interactions mode, that's plip -i 1A0M --peptides B -vx