3dRPC specifications

Information


Unique identifier OMICS_24394
Name 3dRPC
Interface Web user interface
Restrictions to use None
Input data A protein structure file and a RNA structure file.
Input format PDB
Output data A 3D structure.
Output format PDB
Computer skills Basic
Stability No
Source code URL http://biophy.hust.edu.cn/3dRPC.html
Maintained No

Documentation


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Publications for 3dRPC

3dRPC in publications

 (5)
PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] form. based on the murine aptamer, rabal et al. used a three-step bioinformatics process similar to those already discussed, but coupled cluster analysis with their chosen 3d docking algorithm, 3drpc []. clustering algorithm gromacs [] revealed highly populated clusters focused around specific binding sites. in four out of five cases, combining clustering with docking simulation revealed […]

PMCID: 5373608
PMID: 28358834
DOI: 10.1371/journal.pone.0174662

[…] accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. here we propose a pair-conformation-dependent scoring function, 3drpc-score, for 3d rna-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only […]

PMCID: 5546443
PMID: 28388579
DOI: 10.18632/oncotarget.16517

[…] [, ] and the predicted 3d structure of lerna by rna composer web server []. the putative rna structure and the protein hsc70 structure were then docked to generate rna-protein complex decoys by 3drpc [] with default parameters. as shown in figure , lerna interacts with hsc70 nucleotide-binding pocket located at the n-terminal nucleotide binding domain (nbd) through its sequence from site 51 […]

PMCID: 5334405
PMID: 28317012
DOI: 10.1007/s41048-017-0034-y

[…] is a computational method designed for three-dimensional rna–protein complex structure prediction. starting from a protein structure and a rna structure, 3drpc first generates presumptivecomple […]

PMCID: 5220573
PMID: 27892693
DOI: 10.1089/cmb.2016.0128

[…] and assigned a score equal to the number. we evaluated the scoring function using data set ii, a docking benchmark collected by huang and zou (), and compared it with the scoring function used in 3drpc, a state-of-the-art protein–rna docking method developed by huang et al. (). they compared 3drpc with other docking methods using data set ii, and the results showed that 3drpc was better […]


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3dRPC institution(s)
School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
3dRPC funding source(s)
Supported by the NSFC under Grant No. 11374113 and 31570722 and the National High Technology Research and Development Program of China under Grant No. 2012AA020402.

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