Data · dataset · 2013
Regad et al. dataset
Listed in DataCite
Description of the file DataDescription.csv This study is based on a dataset composed of 483 pocket-ligand pairs.
Description
To create a large training set of pocket-ligand pairs, we initially gathered the refined set from the PDBbind database (Wang et al., 2004; 2005) and the Astex test set (Hartshorn et al., 2007) and selected complexes that contained drug-like ligands (i.e. small chemical compounds). Two protein-ligand complex datasets were compiled for the training set.
The first one is composed of 560 non-redundant protein-ligand structures, with a resolution better than 2.5 Å retrieved from the refined set of the PDBbind database. From these structures, we removed those containing metal ions or cofactors next to the co-crystallized ligand resulting in a selection of 432 structures. The second one is composed of 85 manually curated protein-ligand complexes from the Astex test set.
Read the rest (2 more)
As for the previous set, we removed the structures with some ions or cofactors next to the ligand, resulting in a selection of 51 structures. The resulting dataset corresponds at the end to 483 protein-ligand structures. The id and information about each pair are available in the following table DataDescription.csv This table contains:
- PDB code of the complex
- Protein chains containing in the PDB files. If the complex contains several protein chains, their chain Id are separated by "/"
- Amino acid (AA) sequence of each chain. AA sequences correspond to sequence of the crystallized proteins. If the complex contains several protein chains, their AA sequences are separated by "/"
- UniProt Id of each chain. If the complex contains several protein chains, their UniProt Id are separated by "/". NoId means no UniProt Id was find for a given chainSmile code of the interested ligandPDB code of the interested ligandObtained cluster of the pocket-ligand pairs
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Regad_et_al_dataset/662163 ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.662163 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.662163 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.662163 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Computer and information sciences
- From keywords
- Bioinformatics and computational biology
- Inferred from text
- Tabular 65%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.662163 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:computer-and-information-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:tabular | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |