AlphaFold v3.0.1

Version 3.0.1 provides new features, improves performance, improves documentation, and fixes bugs. We thank everyone who reported issues, proposed new features, and submitted PRs!

Change log

Below is a selection of new features, performance improvements and bug fixes. Full change log: v3.0.0...v3.0.1.

New features

• It is now possible to run template-free, but still search for MSA.
• It is now possible to run template search when MSA provided.
• It is now possible to specify MSA and templates as external files instead of inline in the input JSON.
• Added these new flags: --max_template_date, --diffusion_num_samples, --num_recycles, --num_seeds.
• Exposed --conformer_max_iterations as a flag to allow increasing number of RDKit iterations.
• Added an option to return model embeddings and write them to a file.
• Made it possible to set which GPU to use on a multi-GPU system.
• The per-residue pLDDT is now added in the output mmCIF.

Performance improvements

• Replaced the database download script with a significantly faster one and added GCP post-processing scripts.
• Improved the Stockholm converter to not read more sequences than necessary when converting to A3M.
• Improved the Stockholm to A3M conversion to not read the whole file into RAM.
• Sped up template search by not reading and parsing irrelevant mmCIFs. Very significant if PDB stored on a slow filesystem.
• Refactored input JSON parsing as iterator, so that inputs are not all loaded into memory at once and cause an OOM.
• Added sequence deduplication when outputting the JSON, making it smaller for homomers.

Bug fixes

• The data pipeline is now skipped if blank MSA + templates provided.
• Silenced irrelevant Numpy warnings.
• Improved Singularity installation instructions.
• Fixed Pallas GLU kernel on large inputs and updated documentation for compilation buckets.
• Fixed setup to work with Python 3.12.
• If the output directory already exists, AlphaFold won't overwrite files in it, instead it will create a new one.
• Convert DATIVE bond type to SINGLE to match bond types used during training.
• Convert atom element to uppercase in embedding name to match training.
• Fixed user and permissions when untar-ing the PDB mmCIF files.
• Explicitly use conformer_id when getting generated conformers.
• Fixed A3M -> Stockholm conversion when description contains tabs.
• Sort the input files returned by glob - otherwise in arbitrary order.
• Ensure user CCD contains all necessary fields and improve docs.
• Fixed incorrect handling of two-letter atoms in SMILES ligands.
• Use OpenEye canonical SMILES when available.
• Raise clear errors if cannot create molecule definitions.
• Add XLA flag workaround for CUDA Capability 7.x GPUs.
• Small fix for numerical precision when handling PIDs in Pallas kernel.
• Deal properly with non-standard residues in the single-letter sequence.
• Fixed RASA calculation to work with arbitrary chain IDs.
• Use true chain type for paired MSA creation.

We thank the following people for their pull requests and/or great suggestions:
@alchemistcai, @amorehead, @aozalevsky, @ccoulombe, @dailypartita, @DanFosing, @davidecarlson, @eltociear, @hegelab @jkosinski, @jpcartailler, @jpcartailler, @linuxfold, @lucajovine, @noghte, @orbsmiv, @Saharsha-N, @smg3d, @vatese, @YoshitakaMo.