Protein-RNA docking benchmark v1.1

Reference: Pérez-Cano L, Jiménez-García B, Fernández-Recio J. A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data, Proteins. 80(7):1872-82.

The Protein-RNA benchmark v1.1 is composed of 106 cases, with 5 unbound-unbound, 4 unbound-pseudo-unbound, 62 unbound-bound, 5 unbound-model, 8 model-unbound, 19 model-bound cases and 3 model-model. The main objective of this benchmark is to foster the development of new protein-RNA docking algorithms and contribute to the better understanding and prediction of protein-RNA interactions.

Download benchmark:

• .zip file
• .tar.gz file

Updates and corrections

(May, 10, 2013):

1. RNA 1M8W chain is 'c' ('c,e' before)
2. Complex 2PY9 chains are 'a,b:e/f' ('a,b:f' before)
3. Complex 1J2B chains are 'a,b:c/d' ('a,b:c' before)

(Jun, 15, 2021):

1. Links to the PDB corrected.

Version 1.1 (Sep, 15, 2015):

1. 1M8V protein sequence renumbered (thanks to Prof. Shengyou Huang)

^a PDB code of the protein-RNA complex. Protein and RNA chains are separated by colon. Alternative binding modes are separated by a slash ("/").
^b Functional classification of RNA according to SCOR 1.2 database³⁶: 1 = tRNA, 2 = rRNA, 3 = ribozyme, 4 = snRNA, 5 = SRP RNA, 6 = Genetic control elements, 7 = vRNA, 8 = SELEX RNA, 9 = synthetic RNA and 10 = other.
^c PDB code of the protein or RNA subunits.
^d RMSD (Å) between Cα atoms (for proteins) or phosphorous atoms (for RNA) of individual bound reference and unbound structures
^e Buried Surface Area (Ų) of the unbound molecule upon complex formation (see Equation(1) in Methods)
^f RMSD (Å) of interface Cα and phosphorus atoms of unbound protein and RNA structures, and the equivalent atoms in the complex.
^g Unbound RNA is not available or cannot be modelled, so the bound form is used.
^h The biological assembly from the PDB has been considered, therefore some of the chains in the complex have been renamed.

^a PDB code of the protein-RNA complex. Protein and RNA chains are separated by colon. Alternative binding modes are separated by a slash ("/").
^b Functional classification of RNA according to SCOR 1.2 database (36): 1 = tRNA, 2 = rRNA, 3 = ribozyme, 4 = snRNA, 5 = SRP RNA, 6 = Genetic control elements, 7 = vRNA, 8 = SELEX RNA, 9 = synthetic RNA and 10 = other.
^c PDB code of the protein or RNA subunits. Cases in which the protein or RNA has been modelled, the PDB of the template is shown. In italics are shown cases with pseudo-unbound templates, i.e. bound to a different protein or RNA molecule (see main text).
^d RMSD (Å) between Cα atoms (for proteins) or phosphorous atoms (for RNA) of individual bound reference and unbound structures
^e Buried Surface Area (Ų) of the unbound molecule upon complex formation (see Equation(1) in Methods)
^f RMSD (Å) of interface Cα and phosphorus atoms of unbound protein and RNA structures, and the equivalent atoms in the complex.
^g Unbound RNA is not available or cannot be modelled, so the bound form is used.
^h The 24 Nt residues have not been considered for the RMSD calculation as they are swapped between target and template structures and give high RMSDs that do not reflect the true overall quality.
ⁱ The biological assembly from the PDB has been considered, therefore some of the chains in the complex have been renamed.