Work

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (Supplementary Data)

Year: 2023

Type: dataset

Abstract: This dataset contains supplementary replication data for the paper titled "DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction". In particular, it contains a new version of our `final_raw_dips.tar.gz` protein pair representations which now contain (1) residue-level annotations for intrinsic disorder regions (IDRs) as well as (2) a copy of each protein pair representation in the HDF5 file format for programming language-agnostic read capabilities. In addition, this record also contains (3) raw MSAs (in HDF5 file format) generated for each protein pair using Jackhmmer and AlphaFold's small version of the Big Fantastic Database (BFD). Lastly, this record contains (4) PDB metadata derived for each DIPS-Plus complex using Graphein's PDBManager API as well as (5) structure-based (i.e., FoldSeek-based) training and validation splits of the dataset's complexes in the form of respective text files containing the file paths of complexes assigned to each split.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.8071135

Authors: Morehead, Alex, Chen, Chen, Sedova, Ada, Cheng, Jianlin

Institutions: University of Missouri, Oak Ridge National Laboratory

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: National Science Foundation

Awards: III: Medium: Collaborative Research: Guiding Exploration of Protein Structure Spaces with Deep Learning, ABI Innovation: Deep learning methods for protein bioinformatics

OpenAlex ID: W4393519185

Cites:

Cited by: 1

Related to: 10