Computational Structural Biology Lab

Description of the protein-RNA docking benchmark dataset v2.0

 

The downloadable protein-RNA benchmark version 2.0 dataset contains 126 directories, each named according to the protein-RNA complex present in our benchmark. For example, the directory '1asy' corresponds to a protein-RNA complex Aspartyl-tRNA synthetase/ tRNA (ASP). Each of the directories contains the files described below (1asy is taken as example).The files containing the atomic coordinates are in '.pdb' format.

 

1ASY.pdb: This file contains the atomic coordinates of the protein-RNA complex. It is represented by the 4 letter PDB code and contains only those chains that have been used in Table1

 

1EOV.pdb: This file contains the atomic coordinates of the unbound protein structure corresponds to the bound complex 1asy.pdb.

 

2TRA.pdb: This file contains the atomic coordinates of the unbound RNA structure corresponds to the bound complex 1asy.pdb.

 

1ASY_1EOV.pdb: The coordinates of the superposed bound and unbound protein structures are given in this file. The file has been named as the bound structure name followed by the unbound structure.

 

1ASY_2TRA.pdb: Same as above for the superposed bound and unbound RNA structures. The model 1 represents the bound structure and model 2 is the transformed unbound RNA structure.

 

1ASY_mod.pdb: The modified version the protein-RNA complex. Only the residues and nucleotides that are available in the unbound structure are retained in this file. The residues and nucleotides have been renumbered starting from one and the same numbers are followed in the modified unbound PDBs.

 

1EOV_mod.pdb: The modified version of the unbound protein file. Only the residues that are available in the bound structure are retained in this file. The residues have been renumbered starting from one same as the modified bound PDBs.

 

2TRA_mod.pdb: The modified version of the unbound RNA file. Only the nucleotides that are available in the bound structure are retained in this file. The nucleotides have been renumbered starting from one same as the modified bound PDBs.