RosettaCommons/NAKB

Original Paper:

Lawson CL, Berman HM, Vallat B, Chen L, Zirbel C (2024) The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids. Nucleic Acids Research 52, D245-D254.

https://doi.org/10.1093/nar/gkad957

Nucleic Acid Knowledgebase (NAKB)

NAKB data set contains 21166 structures including Nucleic Acids, Protein, and Ligand Annotations, and determined 3D structures found in the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB), including structures determined by X-ray, Electron Microscopy, and Nuclear Magnetic Resonance. Information contained in this data set is PDB/NDB ID, Release Date, Sequence, Polymer Composition, and Molecular Weight. Assemblies, split by chain with sequences added to the curated data of Lawson et al.

Quickstart Usage

Install HuggingFace Datasets package

Each subset can be loaded into python using the Huggingface datasets library. First, from the command line install the datasets library:

$ pip install datasets

then, from within python load the datasets library

import datasets
from datasets import load_dataset

Load model datasets

To load one of the NAKB_sub model datasets:

from datasets import load_dataset

dataset_protein = load_dataset(
    "JOOOOOOOOOOJ/Rosetta_NAKB",
    data_files="Protein/*.csv"
)

dataset_protein["train"].head()

Data Explaination

Each row in the dataset represents a single polymer chain within a larger macromolecular assembly. The dataset includes the following key fields:

• polyclass: The overall assembly classification. This describes the type of macromolecular complex in which the chain is found (e.g., Protein/RNA). It reflects the biological composition of the full structure rather than the individual molecule.

• released: Structure release date.

• resolution: Experimental resolution in Ångströms.

• method: Structure determination method (e.g., EM for electron microscopy).

• chains: Chain identifier within the structure.

• polytype: The polymer type of the individual chain (e.g., Protein, RNA). Unlike polyclass, which describes the entire assembly, polytype refers specifically to the molecular identity of the single chain represented in that row.

• description: Functional or canonical name of the molecule (e.g., ribosomal proteins such as 40S or 60S subunits).

• entityMW: Molecular weight of the entity (kDa).

• seq: Amino acid or nucleotide sequence of the polymer chain.

polyclass vs polytype

It is important to distinguish between the polyclass and polytypeattributes.

polyclass defines the biological assembly category (e.g., a ribonucleoprotein complex composed of proteins and RNA).

polytype defines the chemical nature of the specific chain listed in that row.

For example, in a Protein/RNA polyclass assembly (such as a ribosome), individual rows may have a polytype of Protein (e.g., ribosomal proteins) or RNA (e.g., rRNA chains). Thus, multiple polytypes can exist within a single polyclass. This distinction allows the dataset to represent both the system-level composition of a structure and the molecular identity of its individual components.