Repository Issue Activity (beta)

#697 Feature request: expose PAE (and confidence JSON) in the hosted API output

#659 Error when adding templates in YAML for Boltz2 prediction

#637 affinity.yaml version error

#696 pdb vs mmcif output_format

#587 MSA always rejected as “does not match input sequence” on offline install, even when FASTA and A3M are identical

#695 Request for correction: Boltz manifest draft in OpenSciFlow

#635 asymmetric pair_chains_iptm

#694 ConnectTimeoutError to api.colabfold.com when using Boltz --use_msa_server

#693 ConnectTimeoutErrorwhen fetching fromapi.colabfold.com during high-throughput screening

#689 predict covalent bond using smiles

#629 Too many failed attempts for the MSA generation request

#307 Custom ligands for covalent binding

#632 Single Sequence - Batching and MSA's

#636 CASP16 affinity evaluation reproducibility: paper reports Pearson R(target avg.)=0.65, reproduced ~0.52

#691 [K-Lean] Lean 4 sorry-free contracts for biomolecular structure — ProteinRMSD, TmScore, BoltzmannDistribution

#675 ACE-CYS cyclization fails

#669 Error: list index out of range when adding templates in YAML

#566 Boltz-2 docking with metal cofactor

#396 Question about Offline Model Weight Loading and Feature Extraction for Custom Datasets

#575 Large structure prediction failing: Error "WARNING: ran out of memory, skipping batch"

#541 Problems about structure prediction with Templates

#626 remove pinning of dependencies?

#182 Trunk sampling for increased diversity

#653 CPU runs produce distorted structures with excessively long bonds and colliding atoms

#662 CPU inference produces lower quality predictions due to device-specific autocast bug in boltz2.py