Issues

• Cannot submit the task

  bytedance/Protenix#357 · Filter by author fenavi opened on Oct 15, 2026
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• Which 12 FoldBench-AB interfaces were excluded in the Protenix-v2 report?

  bytedance/Protenix#356 · Filter by author RezaGhi opened on Oct 7, 2026
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• Clarification on Research Use of Protenix-v2 Weights for Modified Inference

  bytedance/Protenix#355 · Filter by author jhpark0805 opened on Sep 30, 2026
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• Do you need Rocm support

  bytedance/Protenix#354 · Filter by author shenshen-amd opened on Sep 28, 2026

• Importance of permutation alignment during training

  bytedance/Protenix#349 · Filter by author andrewliu2001 opened on Sep 2, 2026
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• Cyclic peptide design in Protenix-Server

  bytedance/Protenix#348 · Filter by author aprijal99 opened on Aug 31, 2026
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• JSON template negative indices silently map to trailing residues

  bytedance/Protenix#342 · Filter by author dajiaohuang opened on Aug 22, 2026

• web_service: validate covalent positions against polymer sequence length

  bytedance/Protenix#341 · Filter by author dajiaohuang opened on Aug 22, 2026

• Docs describe unsupported positional arguments for inference_demo.sh

  bytedance/Protenix#340 · Filter by author dajiaohuang opened on Aug 22, 2026

• PairwiseDistancePotential returns NaN autograd gradients for clash-only bounds

  bytedance/Protenix#336 · Filter by author dajiaohuang opened on Aug 22, 2026

• web_service: serialize viewer modifications with inference schema keys

  bytedance/Protenix#335 · Filter by author dajiaohuang opened on Aug 22, 2026

• PyPI project page renders repository-relative README links and images as 404

  bytedance/Protenix#334 · Filter by author dajiaohuang opened on Aug 22, 2026

• Cannot download protenix-v2.pt (HTTP 403)

  bytedance/Protenix#332 · Filter by author cedarice opened on Aug 19, 2026
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• error while trying to use pred command

  bytedance/Protenix#330 · Filter by author hima111997 opened on Jul 31, 2026
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• Protenix Server is hanging

  bytedance/Protenix#329 · Filter by author nil123532 opened on Jul 27, 2026
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• Massive failures occurred after submitting the task

  bytedance/Protenix#327 · Filter by author yaomiaomiao opened on Jul 25, 2026

• Blackwell support

  bytedance/Protenix#326 · Filter by author sistar2020 opened on Jul 6, 2026
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• Error: ColabFold as the MSA source in Protenix

  bytedance/Protenix#324 · Filter by author Midan-midan opened on Jul 2, 2026
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• running in TFG mode with only RNA causes a crash

  bytedance/Protenix#322 · Filter by author seanrjohnson-neb opened on Jun 4, 2026
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• An error occurred during training using Protenix Docker 1.0.0.4

  bytedance/Protenix#321 · Filter by author gs-ren opened on Jun 3, 2026

• setup_databases.sh is taking a very long time during MMseqs2 database setup. Is this expected?

  bytedance/Protenix#320 · Filter by author ReaganGen opened on Jun 2, 2026

• Modelling Proteins with missing residues using template

  bytedance/Protenix#319 · Filter by author EmilyWang1106 opened on May 26, 2026

• Output cif files contains NaN

  bytedance/Protenix#318 · Filter by author guodong1988 opened on May 25, 2026
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• coordinates of OXT sometimes completely off

  bytedance/Protenix#317 · Filter by author CLG68 opened on May 19, 2026

• Some weightedPDB samples cause extremely slow template processing

  bytedance/Protenix#316 · Filter by author clmdy opened on May 12, 2026
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