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Computational Structural Biology Lab
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general
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http://www.csb.iitkgp.ac.in/applications/benchmark.php
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# Computational Structural Biology Lab

**Source**: http://www.csb.iitkgp.ac.in/applications/benchmark.php
**Parent**: http://www.csb.iitkgp.ac.in/

### Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur

- [Home](http://www.csb.iitkgp.ac.in/)
- [Research](http://www.csb.iitkgp.ac.in/pages/research.php)
- [Publications](http://www.csb.iitkgp.ac.in/pages/publications.php)
- [Teaching](http://www.csb.iitkgp.ac.in/pages/teaching.php)
- Tutorials
  - [Python Tutorial](http://www.csb.iitkgp.ac.in/tutorials/python/python_index.php)
  - [Gromacs Tutorial](http://www.csb.iitkgp.ac.in/tutorials/gromacs/gromacs_index.php)
- Tools
  - [PRince](http://www.facweb.iitkgp.ac.in/~rbahadur/prince/home.html)
  - [Layers](http://www.csb.iitkgp.ac.in/applications/mol_layers/main.php)
  - [HotSPRing](http://www.csb.iitkgp.ac.in/applications/HotSPRing/main.php)
  - [NCodR](http://www.csb.iitkgp.ac.in/applications/NCodR/index.php)
  - [Nucpred](http://www.csb.iitkgp.ac.in/applications/Nucpred/index.php)
  - [pmiRScan](http://www.csb.iitkgp.ac.in/applications/pmiRScan/index.php)
  - [proRBR](http://www.csb.iitkgp.ac.in/applications/proRBR/index.php)
  - [Rotamers for RBPs](http://www.csb.iitkgp.ac.in/applications/RBP-Rotamer/rotamer.php)
  - [MetIoR](http://www.csb.iitkgp.ac.in/applications/MetIoR/index.php)
- Databases
  - [PMMLID](http://www.csb.iitkgp.ac.in/databases/miR_details/index.php)
  - [TFNRDv1.0](http://www.csb.iitkgp.ac.in/databases/TFNRDv1.0/tfnrd.html)
  - [ProRBR Dataset](http://www.csb.iitkgp.ac.in/applications/proRBR_dataset/proRBR.php)
- Benchmarks
  - [Protein-RNA Docking Benchmark version 3](http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php)
  - [Protein-RNA Docking Benchmark version 2](http://www.csb.iitkgp.ac.in/applications/PRDBv2.php)
  - [Protein-RNA Docking Benchmark version 1](http://www.csb.iitkgp.ac.in/applications/benchmark.php)
  - [Protein-RNA Affinity Benchmark](http://www.csb.iitkgp.ac.in/applications/PRDBv3/Affinity.php)
- [Members](http://www.csb.iitkgp.ac.in/pages/members.php)
- Links
  - [Bioinformatics Centre](http://www.csb.iitkgp.ac.in/bioinformatics_centre/index.html)
  - [Homepage IITKGP](http://www.iitkgp.ac.in)
  - [Homepage Department of Biotechnology](http://www.bt.iitkgp.ac.in)
- [Contact](http://www.csb.iitkgp.ac.in/pages/contact.php)

**Supplementary Information for Protein RNA benchmark**

Each folder contains
the protein-RNA complex, the unbound structure of protein and
RNA(wherever available;9 cases).

The
transformed coordinates of bound and unbound protein subunits
computed by [DaliLite](http://www.ebi.ac.uk/Tools/dalilite/) and that for RNA subunits computed by [Gromacs](http://www.gromacs.org/) is
also available in the folder.

The
subunits have been filtered and only chains of interest are retained
in the PDB files.

\

[**Click here to download the zipped protein-RNA benchmark**](http://www.csb.iitkgp.ac.in/applications/FINAL_DATABASE.zip)

\

**Table 1. The benchmark dataset of Protein-RNA complexes.**

|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Complex | | | Unbound  (PDB id) | | Interface Area Bb(Å2) | RMSD (Å) | | | Categoryf |
| PDB ida | Protein | RNA | Protein | RNA |  | i-rmsdc | c-rmsdd | p-rmsde |  |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1. Unbound-Unbound    (9)  1. Complexes    with tRNA (3) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1asy](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ASY)  (A:R) | Aspartyl-tRNA synthetase | tRNA (Asp) | [1eov](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EOV)  (A) | [2tra](http://www.rcsb.org/pdb/explore/explore.do?structureId=2TRA)  (A) | 4430 | 1.26 *2.30* | 1.49 | 4.9 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1ttt](http://www.rcsb.org/pdb/explore/explore.do?structureId=1TTT)  (A:D) | Elongation Factor EF-TU | tRNA (Phe) | [1eft](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EFT)  (A) | [4tna](http://www.rcsb.org/pdb/explore/explore.do?structureId=4TNA)  (A) | 2890 | 0.67 *1.32* | 0.69 | 2.5 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2fmt](http://www.rcsb.org/pdb/explore/explore.do?structureId=2FMT)  (A:C) | tRNA-fMet transformylase | tRNA (fMet) | [1fmt](http://www.rcsb.org/pdb/explore/explore.do?structureId=1FMT)  (A) | [3cw6](http://www.rcsb.org/pdb/explore/explore.do?structureId=3CW6)  (A) | 2940 | 0.93 *1.70* | 1.17 | 2.3 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Ribosomal    proteins (1) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1dfu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1DFU)  (P:MN) | Ribosomal protein L25 | 5S rRNA | **[1b75](http://www.rcsb.org/pdb/explore/explore.do?structureId=1B75)**  (A) | [364d](http://www.rcsb.org/pdb/explore/explore.do?structureId=364D)  (ABC) | 1690 | 2.99 *3.73* | 3.00 | 5.3 | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 3. Duplex    RNA (1) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1e7k](http://www.rcsb.org/pdb/explore/explore.do?structureId=1E7K)  (A:C) | Spliceosomal protein 15.5K | U4 snRNA | **[2jnb](http://www.rcsb.org/pdb/explore/explore.do?structureId=2JNB)**  (A) | **[1mfj](http://www.rcsb.org/pdb/explore/explore.do?structureId=1MFJ)**  (A) | 1300 | 0.98 *3.97* | 2.10 | 8.1 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 4. Single-stranded    RNA (4) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1jbs](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JBS)  (A:C) | Sarcin-like cytotoxin Restrictocin | 29-mer SRD RNA analog | [1aqz](http://www.rcsb.org/pdb/explore/explore.do?structureId=1AQZ)  (A) | [1q9a](http://www.rcsb.org/pdb/explore/explore.do?structureId=1Q9A)  (A) | 1310 | 0.59 *1.92* | 0.71 | 3.4 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1wsu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WSU)  (A:E) | Elongation factor SelB | SECIS RNA | [1lva](http://www.rcsb.org/pdb/explore/explore.do?structureId=1LVA)  (A) | **[2rlu](http://www.rcsb.org/pdb/explore/explore.do?structureId=2RLU)**  (A) | 940 | 0.45 *0.77* | 0.70 | 4.6 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1zbh](http://www.rcsb.org/pdb/explore/explore.do?structureId=1zbh)  (AD:E) | 3'-Endonuclease Eri1 | Histone mRNA | [1zbu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZBU)  (AD) | **[1ju7](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ju7)**  (A) | 1760 | 0.62 *1.98* | 0.60 | 4.2 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| **[2b6g](http://www.rcsb.org/pdb/explore/explore.do?structureId=2b6g)**  (A:B) | Vts1p | SRE hairpin RNA | [2d3d](http://www.rcsb.org/pdb/explore/explore.do?structureId=2d3d)  (A) | **[2b7g](http://www.rcsb.org/pdb/explore/explore.do?structureId=2b7g)**  (A) | 483 | 0.29 *0.89* | 0.90 | 2.47 | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Unbound-Bound    (36)  1. Complexes    with tRNA (13) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1c0a](http://www.rcsb.org/pdb/explore/explore.do?structureId=1c0a)  (A:B) | Aspartyl-tRNA synthetase | tRNA (Asp) | [1eqr](http://www.rcsb.org/pdb/explore/explore.do?structureId=1eqr)  (A) | - | 4180 | 1.60 | 1.63 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1f7u](http://www.rcsb.org/pdb/explore/explore.do?structureId=1f7u)  (A:B) | Arginyl-tRNA synthetase | tRNA (Arg) | [1bs2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1BS2)  (A) | - | 5140 | 2.17 | 2.00 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1h4s](http://www.rcsb.org/pdb/explore/explore.do?structureId=1h4s)  (AB:T) | Prolyl-tRNA synthetase | tRNA (Pro) | [1hc7](http://www.rcsb.org/pdb/explore/explore.do?structureId=1hc7)  (AB) | - | 2480 | 0.95 | 1.02 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1j1u](http://www.rcsb.org/pdb/explore/explore.do?structureId=1j1u)  (AA':B) | Tyrosyl-tRNA synthetase | tRNA (Tyr) | [1u7d](http://www.rcsb.org/pdb/explore/explore.do?structureId=1u7d)  (AB) | - | 2240 | 0.77 | 1.27 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1n78](http://www.rcsb.org/pdb/explore/explore.do?structureId=1n78)  (A:C) | Glutamyl-tRNA synthetase | tRNA (Glu) | [1j09](http://www.rcsb.org/pdb/explore/explore.do?structureId=1j09)  (A) | - | 4510 | 1.44 | 1.87 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1qf6](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QF6)  (A:B) | Threonyl-tRNA synthetase*.* | tRNA (Thr) | [1evl](http://www.rcsb.org/pdb/explore/explore.do?structureId=1EVL)  (A) | - | 4230 | 0.74 | 0.80 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1qtq](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QTQ)  (A:B) | Glutaminyl-TRNA synthetase | tRNA (Gln) | [1nyl](http://www.rcsb.org/pdb/explore/explore.do?structureId=1NYL)  (A) | - | 5200 | 1.85 | 1.62 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1ser](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SER)  (AB:T) | Seryl-tRNA Synthetase | tRNA (Ser) | [1ses](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ses)  (AB) | - | 2290 | 2.44 | 1.69 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1u0b](http://www.rcsb.org/pdb/explore/explore.do?structureId=1u0b)  (B:A) | Cysteinyl-tRNA synthetase | tRNA (Cys) | [1li5](http://www.rcsb.org/pdb/explore/explore.do?structureId=1li5)  (B) | - | 4560 | 0.96 | 0.66 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2azx](http://www.rcsb.org/pdb/explore/explore.do?structureId=2azx)  (AA':C) | Tryptophanyl-tRNA synthetase | tRNA (Trp) | [1r6u](http://www.rcsb.org/pdb/explore/explore.do?structureId=1r6u)  (AB) | - | 2130 | 0.59 | 0.81 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2bte](http://www.rcsb.org/pdb/explore/explore.do?structureId=2bte)  (A:B) | Leucyl-tRNA synthetase | tRNA (Leu) | [1obc](http://www.rcsb.org/pdb/explore/explore.do?structureId=1obc)  (A) | - | 3430 | 1.34 | 1.2 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2drb](http://www.rcsb.org/pdb/explore/explore.do?structureId=2drb)  (A:B) | CCA-adding enzyme | tRNA (35-mer) | [1uet](http://www.rcsb.org/pdb/explore/explore.do?structureId=1uet)  (A) | - | 3200 | 1.75 | 1.06 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2fk6](http://www.rcsb.org/pdb/explore/explore.do?structureId=2fk6)  (A:R) | RNase Z | tRNA (Thr) | [1y44](http://www.rcsb.org/pdb/explore/explore.do?structureId=1y44)  (A) | - | 1530 | 0.83 | 0.74 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Ribosomal    proteins (2) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1sds](http://www.rcsb.org/pdb/explore/explore.do?structureId=1sds)  (C:FF') | Ribosomal protein L7Ae | box H/ACA sRNA | [1xbi](http://www.rcsb.org/pdb/explore/explore.do?structureId=1xbi)  (A) | - | 1200 | 0.37 | 0.33 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2hw8](http://www.rcsb.org/pdb/explore/explore.do?structureId=2hw8)  (A:B) | Ribosomal protein L1 | mRNA | [1ad2](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ad2)  (A) | - | 2330 | 5.06 | 6.67 | - | X |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 3. Duplex    RNA (9) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1msw](http://www.rcsb.org/pdb/explore/explore.do?structureId=1msw)  (D:R) | RNA polymerase, phage T7 | 17-nucleotide RNA transcript | [1aro](http://www.rcsb.org/pdb/explore/explore.do?structureId=1aro)  (P) | - | 1830 | 3.55 | 3.5 | - | X |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1r3e](http://www.rcsb.org/pdb/explore/explore.do?structureId=1r3e)  (A:CDE) | Pseudo-U synthetase TruB | 17- nucleotide RNA | [1ze1](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ze1)  (A) | - | 3280 | 3.34 | 2.0 | - | X |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1wne](http://www.rcsb.org/pdb/explore/explore.do?structureId=1wne)  (A:BC) | RNA polymerase, FMD virus | template-primer RNA decanucleotide | [1u09](http://www.rcsb.org/pdb/explore/explore.do?structureId=1u09)  (A) | - | 3080 | 0.62 | 0.70 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1yvp](http://www.rcsb.org/pdb/explore/explore.do?structureId=1yvp)  (B:EFH) | Ro autoantigen | Y RNA | [1yvr](http://www.rcsb.org/pdb/explore/explore.do?structureId=1yvr)  (A) | - | 3500 | 1.26 | 1.44 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1zbi](http://www.rcsb.org/pdb/explore/explore.do?structureId=1zbi)  (A:CD) | RNase H | A form RNA | [1zbf](http://www.rcsb.org/pdb/explore/explore.do?structureId=1zbf)  (A) | - | 3210 | 0.63 | 0.56 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2az0](http://www.rcsb.org/pdb/explore/explore.do?structureId=2az0)  (AB:CD) | Flock House virus protein B2 | siRNA | **[2b9z](http://www.rcsb.org/pdb/explore/explore.do?structureId=2b9z)**  (AB) | - | 1970 | 1.01 | 1.30 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2ez6](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ez6)  (AB:CD) | RNase III | dsRNA | [1jfz](http://www.rcsb.org/pdb/explore/explore.do?structureId=1jfz)  (AB) | - | 5190 | 0.77 | 1.00 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2f8s](http://www.rcsb.org/pdb/explore/explore.do?structureId=2f8s)  (A:CD) | Argonaute protein | siRNA | [1yvu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1yvu)  (A) | - | 990 | 1.53 | 1.90 | - | S |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2gjw](http://www.rcsb.org/pdb/explore/explore.do?structureId=2gjw)  (AB:EFH) | Splicing endonuclease | BHB RNA | [1r0v](http://www.rcsb.org/pdb/explore/explore.do?structureId=1r0v)  (AB) | - | 2620 | 1.02 | 0.95 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 4. Single-stranded    RNA (12) | | | | | | | | | |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1k8w](http://www.rcsb.org/pdb/explore/explore.do?structureId=1k8w)  (A:B) | Pseudo-U synthetase TruB | T stem-loop RNA | [1r3f](http://www.rcsb.org/pdb/explore/explore.do?structureId=1r3f)  (A) | - | 2610 | 1.27 | 1.90 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1m5o](http://www.rcsb.org/pdb/explore/explore.do?structureId=1m5o)  (C:B) | U1 SnpA Ribozyme | Hairpin ribozyme | [1oia](http://www.csb.iitkgp.ac.in/applications/:http:/www.rcsb.org/pdb/explore/explore.do?structureId=1oia)  (A) | - | 1770 | 0.91 | 1.20 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1m8v](http://www.rcsb.org/pdb/explore/explore.do?structureId=1m8v)  (AM:O) | Sm like protein | Uridine heptamer | [1h64](http://www.rcsb.org/pdb/explore/explore.do?structureId=1h64)  (AM) | - | 1290 | 0.37 | 0.60 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1m8w](http://www.rcsb.org/pdb/explore/explore.do?structureId=1m8w)  (A:C) | PH domain | Nre1-19 RNA | [1m8z](http://www.rcsb.org/pdb/explore/explore.do?structureId=1m8z)  (A) | - | 2110 | 0.75 | 0.80 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1n35](http://www.rcsb.org/pdb/explore/explore.do?structureId=1n35)  (A:BC) | RNA polymerase lambda3, reovirus | dsRNA | [1muk](http://www.rcsb.org/pdb/explore/explore.do?structureId=1muk)  (A) | - | 3240 | 0.94 | 0.50 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [1wpu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1wpu)  (A:C) | Hutp antiterminator | Hut mRNA | [1wpv](http://www.rcsb.org/pdb/explore/explore.do?structureId=1wpv)  (A) | - | 1360 | 0.17 | 0.23 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2a8v](http://www.rcsb.org/pdb/explore/explore.do?structureId=2A8V)  (B:E) | RHO transcription termin. factor | Cytosine-rich RNA | [1a8v](http://www.rcsb.org/pdb/explore/explore.do?structureId=1A8V)  (B) | - | 720 | 1.62 | 1.00 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2asb](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ASB)  (A:B) | NusA antiterminator | BoxC rRNA | [1k0r](http://www.rcsb.org/pdb/explore/explore.do?structureId=1K0R)  (A) | - | 2320 | 0.82 | 1.08 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2bgg](http://www.rcsb.org/pdb/explore/explore.do?structureId=2BGG)  (A:PQ) | PIWI protein | siRNA | [1w9h](http://www.rcsb.org/pdb/explore/explore.do?structureId=1W9H)  (A) | - | 2240 | 0.76 | 0.90 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2bh2](http://www.rcsb.org/pdb/explore/explore.do?structureId=2BH2)  (A:C) | Methyltransferase RumA | 23S rRNA | [1uwv](http://www.rcsb.org/pdb/explore/explore.do?structureId=1UWV)  (A) | - | 4040 | 0.67 | 1.41 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2gic](http://www.rcsb.org/pdb/explore/explore.do?structureId=2GIC)  (A:R) | VSV nucleocapsid | Viral genomic RNA | [2qvj](http://www.rcsb.org/pdb/explore/explore.do?structureId=2QVJ)  (A) | - | 2000 | 0.88 | 1.30 | - | R |
|  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| [2ix1](http://www.rcsb.org/pdb/explore/explore.do?structureId=2IX1)  (A:B) | RNase II | Single-stranded RNA | [2ix0](http://www.rcsb.org/pdb/explore/explore.do?structureId=2IX0)  (A) | - | 4160 | 0.94 | 1.59 | - | S |

\

aFour-letter
PDB code of the protein-RNA complexes used in the dataset with the
chain ID(s) of the protein and the RNA molecules in the parentheses.
Structures solved with NMR spectroscopy method are shown in bold.
Symmetry-related chains are primed (e.g. A' in 1j1u).

bSurface
area buried between protein and RNA upon complexation.

RMSD was calculated
over the cC&alpha
atoms of the interface residues, while the values in italics include
the phosphorus atoms of the interface nucleotides when the
corresponding free RNA structure is available; dAll
C&alpha
atoms of the protein chain; eAll
phosphorus atoms of the RNA chain when the unbound structure of the
same is available.

fDifferent
categories according to the expected difficulty for the protein-RNA
docking algorithm: (R) Rigid body, (S)Semi flexible and (X) Full
flexible.

\