ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries

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).