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Hardcoded PeptideL causes pipeline failure on Protein-DNA complexes (e.g. 3K5M)

Status: Open.

#43 In apple/ml-simplefold;

· xinyuren-bio opened on Dec 24, 2025

Question on reference conformers used and training protocol

questionFurther information is requestedFurther information is requested

Status: Open.

#41 In apple/ml-simplefold;

· FranklinHu1 opened on Dec 8, 2025

Inconsistent data in ccd.pkl and ccd.rdb

questionFurther information is requestedFurther information is requested

Status: Open.

#38 In apple/ml-simplefold;

· zxyHappy opened on Nov 13, 2025

How can I download the AFESM structure files?

questionFurther information is requestedFurther information is requested

Status: Open.

#37 In apple/ml-simplefold;

· fengshikun opened on Nov 11, 2025

FASTA with multiple entries

questionFurther information is requestedFurther information is requested

Status: Open.

#35 In apple/ml-simplefold;

· fjell-dev opened on Nov 3, 2025

Tool accessibility: allow use of simplefold script outside of the installed repo

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#33 In apple/ml-simplefold;

· sterrettjd-idt opened on Oct 30, 2025

How to get the benchmark dataset for evaluation ?

questionFurther information is requestedFurther information is requested

Status: Open.

#32 In apple/ml-simplefold;

· tangshixiang opened on Oct 30, 2025

Domain overlaps (pseudokinase domains overlap kinase domains)

questionFurther information is requestedFurther information is requested

Status: Open.

#29 In apple/ml-simplefold;

· ljmartin opened on Oct 24, 2025

JAX/Flax NNX implementation of SimpleFold

enhancementNew feature or requestNew feature or request

Status: Open.

#28 In apple/ml-simplefold;

· SjoerdWiarda opened on Oct 23, 2025

OOM error on NVIDIA A100

questionFurther information is requestedFurther information is requested

Status: Open.

Bug

#24 In apple/ml-simplefold;

· iamysk opened on Oct 15, 2025

Kernel Crash (Exit Code 3221225477) when loading pLDDT model

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#19 In apple/ml-simplefold;

· tangyuhao8 opened on Oct 10, 2025

ESM checkpoints

questionFurther information is requestedFurther information is requested

Status: Open.

Feature

#18 In apple/ml-simplefold;

· rrw1007 opened on Oct 1, 2025