Issues

• Inquiry regarding significant score variance in zero-shot mutation prediction

  westlake-repl/SaProt#98 · Filter by author bingjielu opened on Apr 8, 2026
  1

• How to use SaProt as a binary classification embedding in a proper way？

  westlake-repl/SaProt#96 · Filter by author KyrieYsPKU opened on Sep 24, 2025
  2

• Error about mutation_zeroshot.py

  westlake-repl/SaProt#95 · Filter by author rescuz opened on Sep 2, 2025
  5

• More evaluation metrics

  westlake-repl/SaProt#93 · Filter by author kalifadan opened on Jun 22, 2025
  1

• How to extract whole-protein structural representations with multi-chain input?

  westlake-repl/SaProt#92 · Filter by author ShenAoAO opened on Jun 19, 2025
  4

• foldseek of beta-lactamase

  westlake-repl/SaProt#90 · Filter by author onebluesky37 opened on Apr 18, 2025
  3

• How to use GO dataset?

  westlake-repl/SaProt#89 · Filter by author tuvefou opened on Apr 17, 2025
  3

• How to select mutation sites for wet experiment

  westlake-repl/SaProt#88 · Filter by author lsy-199612 opened on Apr 16, 2025
  3

• Reproduce Results

  westlake-repl/SaProt#82 · Filter by author kalifadan opened on Jan 12, 2025
  7

• 1) sequence recovery (sequence design) code request 2) generating .mdb file 3) PEFT 4) best model selection after training

  westlake-repl/SaProt#73 · Filter by author sj584 opened on Nov 18, 2024
  1

• How to fine tune locally with SaProtHub datasets?

  westlake-repl/SaProt#72 · Filter by author dc2211 opened on Nov 14, 2024
  11

• LightingModule optimizer issue - Thermostability fine-tuning

  westlake-repl/SaProt#71 · Filter by author dc2211 opened on Nov 13, 2024
  5

• finetuning with MLM task

  westlake-repl/SaProt#70 · Filter by author sj584 opened on Oct 30, 2024
  5

• code for pretraining

  westlake-repl/SaProt#67 · Filter by author done520 opened on Oct 6, 2024
  1

• PDB Validation set for figure 2

  westlake-repl/SaProt#61 · Filter by author alex-hh opened on Sep 23, 2024
  1

• KeyError: 'XcXgXyXtXyXgXd

  westlake-repl/SaProt#59 · Filter by author 1412140736 opened on Sep 7, 2024
  1

• the results of DMS fitness in the ProteinGym benchmark

  westlake-repl/SaProt#57 · Filter by author jiaolifengmi opened on Aug 21, 2024
  1

• Temperature (pLDDT) masking for multiple chain PDB files

  westlake-repl/SaProt#55 · Filter by author Hrovatin opened on Aug 14, 2024
  4

• Model use - relative imports

  westlake-repl/SaProt#54 · Filter by author Hrovatin opened on Aug 14, 2024
  4

• fine-tuning with more protein sequences

  westlake-repl/SaProt#53 · Filter by author avilella opened on Aug 13, 2024
  10

• How to use SaProt as an encoder just like esm

  westlake-repl/SaProt#52 · Filter by author KyrieYsPKU opened on Aug 12, 2024
  1

• Inconsistency in number of classes in EC/GO downstream datasets

  westlake-repl/SaProt#50 · Filter by author klemens-floege opened on Jul 31, 2024
  1

• Contact map prediction

  westlake-repl/SaProt#48 · Filter by author gezmi opened on Jul 16, 2024
  1

• can not use foldseek

  westlake-repl/SaProt#47 · Filter by author WenxiangL opened on Jul 11, 2024
  1

• Training SaProt with a smaller ESM model

  westlake-repl/SaProt#45 · Filter by author BSharmi opened on Jul 6, 2024
  3