Sold by: Louisiana State University
Open data
|
Deployed on AWS
DPEB is a multimodal database of human protein embeddings integrating four biologically complementary representations—AlphaFold2, BioEmbeddings, ESM-2, and ProtVec—designed for enhanced protein-protein interaction prediction and functional classification.
Overview
DPEB is a multimodal database of human protein embeddings integrating four biologically complementary representations—AlphaFold2, BioEmbeddings, ESM-2, and ProtVec—designed for enhanced protein-protein interaction prediction and functional classification.
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
- Multimodal human protein embeddings (AlphaFold2, BioEmbeddings, ESM-2, ProtVec) with JSONL-formatted metadata containing FASTA, UniProt IDs, and embeddings.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::deepdrug-dpeb
- AWS region
- us-west-2
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://deepdrug-dpeb/
Resources
Vendor resources
Support
Managed By
Louisiana State University
How to cite
DeepDrug Protein Embeddings Bank (DPEB) was accessed on DATE from https://registry.opendata.aws/deepdrug-dpeb .
License
MIT
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The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligands present in the entry, details about the structure-determination experiment, authors and publication information, experimental data, and the wwPDB validation report. Additional content stored in the archive includes documentation, summary reports, and software (among others).
The PDB is a jointly-managed core archive of the Worldwide Protein Data Bank partnership [RCSB Protein Data Bank (RCSB PDB, rc[...]
BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions. The structure data are collected primarily from the Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. BioLiP aims to construct the most comprehensive and accurate database for serving the needs of ligand-protein docking, virtual ligand screening and protein function annotation.