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README
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README
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PROTEIN-RNA BENCHMARK V1.0 README FILE
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Thanks for downloading the Protein-RNA benchmark v1.0. This benchmark 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 and 3 model-model cases. You will find here the directories corresponding to all these cases, named according to their complex PDB references:
- unbound-unbound/ --> 1ASY/ 1DFU/ 1OB2/ 1R3E/ 2FMT/
- unbound-pseudo-unbound/ --> 1B23/ 1MFQ/ 1QTQ/ 1U0B/
- unbound-bound/ --> 1B7F/ 1C9S/ 1DK1/ 1E7K/ 1EC6/ 1EIY/ 1EKZ/ 1F7U/ 1G1X/ 1H3E/ 1H4S/ 1HC8/ 1HVU/
1JBR/ 1K8W/ 1KOG/ 1KQ2/ 1M5O/ 1M8V/ 1M8W/ 1MMS/ 1N78/ 1Q2R/ 1SER/ 1T0K/ 1T4L/
1U63/ 1WNE/ 1WPU/ 1WSU/ 1YVP/ 2AD9/ 2ADB/ 2ADC/ 2ASB/ 2AZ0/ 2AZX/ 2BGG/ 2BH2/
2BTE/ 2BU1/ 2C0B/ 2CZJ/ 2ERR/ 2F8K/ 2FK6/ 2GIC/ 2GJE/ 2GJW/ 2HGH/ 2HW8/ 2I91/
2IX1/ 2PY9/ 2QUX/ 2R7R/ 3BO2/ 3BSB/ 3BSO/ 3BSX/ 3BX2/ 3CIY/
- unbound-model/ --> 1C0A/ 1EFW/ 1J1U/ 1J2B/ 1VFG/ 2DRA/
- model-unbound/ --> 1FEU/ 1HQ1/ 1LNG/ 1OOA/ 1RKJ/ 2R8S/ 2V3C/ 2ZKO/
- model-bound/ --> 1DDL/ 1E8O/ 1FXL/ 1K1G/ 1RLG/ 2B3J/ 2CJK/ 2D6F/ 2DB3/ 2DER/ 2FY1/ 2I82/ 2IPY/ 2JPP/ 2NUG/
- model-model/ --> 1QF6/ 1VFG/ 2DU3/
Within each directory you will find the following files (XXXX represents the corresponding directory name for each case):
- XXXX_complex.pdb The unmodified coordinates of the considered protein and RNA chains from the complex RCSB PDB file
- XXXX_complex.fasta The FASTA format sequences of the considered protein and RNA chains from the complex RCSB PDB file
- XXXX_prot.pdb The unmodified coordinates of the considered protein chain/s from the protein unbound RCSB PDB file or coordinates
from the protein model pdb (for model-unbound, model-bound or model-model cases)
- XXXX_prot.fasta The FASTA format sequence/s of the considered protein chain/s from the protein unbound RCSB PDB file or input FASTA format sequence/s from the complex RCSB PDB file used for building the protein homology model (for model-unbound, model-bound or model-model cases)
- XXXX_prot.resnum Residue numbering correspondence between complex and individual protein structures
- XXXX_RNA.pdb The unmodified coordinates of the considered RNA chain/s from the RNA unbound RCSB PDB file or coordinates from the
complex RCSB PDB file (for unbound-bound or model-bound cases) or from the RNA model pdb (for unbound-model or model-model cases)
- XXXX_RNA.fasta The FASTA format sequence/s of the considered RNA chain/s from the RNA unbound RCSB PDB file or from the
complex RCSB PDB file (for unbound-bound, model-bound and for unbound-model or model-model cases as the input sequences for the modelling)
- XXXX_RNA.resnum Residue numbering correspondence between complex and individual RNA structures
In unbound-model, model_unbound, model-bound and model-model directories you can also find the following files:
- XXXX_PROTtemplate.pdb The unmodified coordinates of the considered protein chain/s from the template RCSB PDB file
- XXXX_PROTtemplate.fasta The FASTA format sequence/s of the considered protein chain/s from the template RCSB PDB file
- XXXX_prot-template.ali The alignment of protein and template sequences used for modelling the unbound protein structure
- XXXX_RNAtemplate.pdb The unmodified coordinates of the considered RNA chain/s from the template RCSB PDB file
- XXXX_RNAtemplate.fasta The FASTA format sequence/s of the considered RNA chain/s from the template RCSB PDB file
- XXXX_RNA-template.ali The alignment of RNA and template sequences used for modelling the unbound RNA structure
You can contact Juan Fernández-Recio for questions or suggestions at [email protected]