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Dataset Open Access

ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries

Moniot, Antoine; Guermeur, Yann; De Vries, Sjoerd Jacob; Chauvot de Beauchene, Isaure

This archive contains data obtained by running the ProtNAff pipeline (https://github.com/isaureCdB/ProtNAff) and used to perform the analyses described in the original ProtNAff paper. The input list of PDB IDs was obtained in October 2021 by searching all PDB structures that contain protein chains and RNA chains but no DNA, and where the resolution is less than 3 A or where the method is NMR. The ribosomes are removed from this database due to their size.

The files provided are:

- structures.json : the database containing metadata and parsing data for all the protein-RNA structures from the input list

- fragments_clust.json : the list and description of all the trinucleotide fragments extracted from those structures

- trinucl_clust1A_allatom: the all-atom coordinates of the trinucleotide fragment library , i.e. the centers of 1A clusters such that each initial fragment has a RMSD of less than 1A from at least one of those centers.

- trinucl_clust1A_ATTRACT: the coordinates of the trinucleotide fragment library , but reduced into ATTRACT coarse-grained representation (Setny and Zacharias, NAR 2011).

Files (303.8 MB)
Name Size
fragments_clust.json
md5:e8c0ee03790653e0b8b168229978b7cb
49.2 MB Download
npy2pdb.py
md5:fa19d39c962a9e984a1f70d652dee8c4
3.0 kB Download
pdb_templates.tgz
md5:55cd840e88f90d43e4d75a903615afec
38.4 kB Download
README
md5:e373124c6be77d65e17f6f3b977aa645
1.5 kB Download
structures.json
md5:a63bc91c852676e66bb280e169fac000
55.2 MB Download
trinucl_clust1A_allatom.tar
md5:4916dfc5608ac9247353c7c5517f039e
171.9 MB Download
trinucl_clust1A_ATTRACT.tar
md5:c57464b7315e3dcba88df19faf82cb15
27.5 MB Download
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