RerankOut.exe interaction with antivirus

[Arthfael]

What does RerankOut.exe do? Last Friday, after I installed pLink 3 and successfully ran it a couple of times, this file seemed to do something which my antivirus found to be suspicious. Since then, I have not been able to use pLink 3, it encounters an error when running. It seems likely that the issue is this missing file. I have tried a fresh installation but every time when I try to launch pLink 3 now the antivirus immediately says it did something suspicious and deletes the file again.
Antivirus log:
13/06/2026 00:38:56;Real-time file system protection;file;C:\pFindStudio\pLink\3.0.17\bin\RerankOut\RerankOut.exe;Suspicious Object;cleaned by deleting;NT AUTHORITY\SYSTEM;Event occurred during an attempt to access the file by the application: C:\Windows\System32\CompatTelRunner.exe (2E34E7DC68065F23835F2284DABA918573FE6F35).;588F6DBD31F0B80ECC96C80DB0E13E0E2A7DC50D;06/05/2025 15:16:28;S-1-5-18;;ad4fkcc6702johfCYcZGvw==

[NorthblueM]

RerankOut.exe is the re-scoring module in pLink 3, and it is very helpful for improving the identification of inter-protein cross-links.

RerankOut.exe itself does not contain any viruses; this is a false positive from the antivirus software. This issue is primarily caused by certain Python modules in pLink 3 being packaged using PyInstaller. Similar antivirus false-positive detections have been widely reported in the official PyInstaller repository: pyinstaller antivirus-false-positives.

Other pLink 3 modules that may be affected include:

• ./pParse2Plus/pParse2Plus.exe
• ./MultiProcess/MultiProcess.exe
• ./RerankOut/RerankOut.exe
• ./pLinkFDR/pLinkFDR.exe

If any of the above .exe files are missing, please restore them from your antivirus quarantine and add them to the whitelist/exclusion list. Alternatively, you can add the bin folder in the pLink 3 installation directory to the whitelist/exclusion list of your antivirus software.

Please rest assured that pLink 3 does not contain any malicious source code.