RNApdbee protocols

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RNApdbee specifications

Information


Unique identifier OMICS_03950
Name RNApdbee
Interface Web user interface
Restrictions to use None
Input format PDB,BPSEQ,CT
Output format BPSEQ,CT
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Marta Szachniuk <>

Additional information


http://rnapdbee.cs.put.poznan.pl/help

Publications for RNApdbee

RNApdbee in pipeline

2017
PMCID: 5570162
PMID: 28472503
DOI: 10.1093/nar/gkx365

[…] multiple sequence alignments. varna () allows for interactive drawing and editing of rna secondary structures. assemble () combines rna secondary structure design with 3d modeling. moreover, rnapdbee () extracts rna secondary structure from 3d coordinates, and presents it in planar diagrams. none of these tools, however, has the capability of selecting common rna structural features […]


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RNApdbee in publications

 (3)
PMCID: 5570162
PMID: 28472503
DOI: 10.1093/nar/gkx365

[…] multiple sequence alignments. varna () allows for interactive drawing and editing of rna secondary structures. assemble () combines rna secondary structure design with 3d modeling. moreover, rnapdbee () extracts rna secondary structure from 3d coordinates, and presents it in planar diagrams. none of these tools, however, has the capability of selecting common rna structural features […]

PMCID: 4619022
PMID: 26488894
DOI: 10.1371/journal.pone.0139476

[…] [] to those base pairs determined by rnaview from the tertiary pdb structure, resulting in the secondary structure having a largest number of base pairs (one could alternatively use the web server rnapdbee []). we also consider the corresponding versions of relative contact order, by dividing the absolute contact order by rna sequence length., for benchmarking purposes, we took two datasets: […]

PMCID: 4557229
PMID: 26329823
DOI: 10.1186/s12859-015-0718-6

[…] implementation, this was achieved by integrating the functionality of two fully automated, high fidelity methods in a computational pipeline: rnacomposer for the 3d rna structure prediction and rnapdbee for base-pair annotation., the presented methodology ties together existing applications for rna 3d structure prediction and base-pair annotation. the example performance, applying […]


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RNApdbee institution(s)
Institute of Computing Science, Poznan University of Technology, Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Poznan Supercomputing and Networking Center, Poznan, Poland
RNApdbee funding source(s)
Supported by the National Science Center, Poland (2016/23/B/ ST6/03931) and Faculty of Computing, Poznan University of Technology, within intramural financing program (09/91/DSPB/0628).

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