Sold by: OpenFold Consortium
Open data
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Deployed on AWS
This dataset contains MSAs and predicted structures used to train OpenFold3 preview, an open-source, all-atom ligand, RNA and protein structure prediction software. This includes -
- PDB - 245k structures and alignments from the RCSB Protein Data Bank - https://www.rcsb.org/
- Long monomer distillation set - ~13 million long (sequence length >= 200 amino acids) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/.
- Short monomer distillation set - 400k short (sequence length < 200 amino acid) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/.
- Disordered set - AF2-predicted structures for unresolved segments missing from the PDB
- RNA - OF3p2-predicted RNA monomer structures generated from a clustered version of RFAM (current version)
For the distillation sets MSAs were generated using the AF3 protocol, and were used to predict structures with AlphaFold2, more details can be found in our whitepaper - https://portal.openfold.om[...]
Overview
This dataset contains MSAs and predicted structures used to train OpenFold3 preview, an open-source, all-atom ligand, RNA and protein structure prediction software. This includes -
- PDB - 245k structures and alignments from the RCSB Protein Data Bank - https://www.rcsb.org/
- Long monomer distillation set - ~13 million long (sequence length >= 200 amino acids) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/ .
- Short monomer distillation set - 400k short (sequence length < 200 amino acid) monomers from the MGNIFY database - https://www.ebi.ac.uk/metagenomics/ .
- Disordered set - AF2-predicted structures for unresolved segments missing from the PDB
- RNA - OF3p2-predicted RNA monomer structures generated from a clustered version of RFAM (current version) For the distillation sets MSAs were generated using the AF3 protocol, and were used to predict structures with AlphaFold2, more details can be found in our whitepaper - https://portal.openfold.omsf.io/reports/of3p2_technical_report.pdf For a full description and an interactive data explorer, please visit https://portal.openfold.omsf.io/datasets
Features and programs
Open Data Sponsorship Program
This dataset is part of the Open Data Sponsorship Program, an AWS program that covers the cost of storage for publicly available high-value cloud-optimized datasets.
Pricing
This is a publicly available data set. No subscription is required.
Legal
Content disclaimer
Vendors are responsible for their product descriptions and other product content. AWS does not warrant that vendors' product descriptions or other product content are accurate, complete, reliable, current, or error-free.
Delivery details
AWS Data Exchange (ADX)
AWS Data Exchange is a service that helps AWS easily share and manage data entitlements from other organizations at scale.
Open data resources
Available with or without an AWS account.
- How to use
- To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more
- Description
- A repository of MSAs and 3D protein structural coordinates used to train OpenFold3.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::openfold3-data
- AWS region
- us-west-2
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://openfold3-data/
Resources
Vendor resources
Support
Managed By
OpenFold Consortium
How to cite
OpenFold3 Training Data was accessed on DATE from https://registry.opendata.aws/openfold3 .
License
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