User:Wayne Decatur/Structure analysis tools

From Proteopedia

Jump to: navigation, search

Contents

Nucleic acid in general

  • Curves+ is a revised version of the Curves approach for analyzing the structure of nucleic acids. The webserver form can be accessed here where citations of the related articles are in another tab. There seems to be a command line-based one in Fortran available here.
  • Despite what the name original stood for, DSSR handles nucleic acids in general as well. See the description below for links.


RNA specific

  • DSSR -(Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. PMID: 26184874 [2] (Maybe name of given supplemental data file previously DSSR stood for "DSSR_ a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates".? Jmol now has integrated real time updates to data generated by DSSR, see here and a 2017 article on it here[3].
  • RNApdbee -a webserver to derive secondary structures from PDB files of knotted and unknotted RNAs PMID: 24771339[4]. Use it here.


Mutations

Related


Python-based utilities

  • seqmagick-An imagemagick-like frontend to Biopython SeqIO. For example, it can convert from fasta to phylip, remove gaps from a fasta-formatted sequence, and describe all FASTA files in the current directory. Requires Biopython.
  • see also on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use
  • click `launch binder` here for a series of demonstrations of useful resources on command line for manipulating structure files.

R-based utilities

My own structure work-related code

  • Structure/model manipulation Python code
  • see also on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use
  • click `launch binder` here for a series of demonstrations of useful resources on command line for manipulating structure files.


References

  1. Mizianty MJ, Fan X, Yan J, Chalmers E, Woloschuk C, Joachimiak A, Kurgan L. Covering complete proteomes with X-ray structures: a current snapshot. Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2781-93. doi:, 10.1107/S1399004714019427. Epub 2014 Oct 23. PMID:25372670 doi:http://dx.doi.org/10.1107/S1399004714019427
  2. Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res. 2015 Dec 2;43(21):e142. doi: 10.1093/nar/gkv716. Epub 2015 Jul, 15. PMID:26184874 doi:http://dx.doi.org/10.1093/nar/gkv716
  3. Hanson RM, Lu XJ. DSSR-enhanced visualization of nucleic acid structures in Jmol. Nucleic Acids Res. 2017 May 3. doi: 10.1093/nar/gkx365. PMID:28472503 doi:http://dx.doi.org/10.1093/nar/gkx365
  4. Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M. RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W368-72. doi:, 10.1093/nar/gku330. Epub 2014 Apr 25. PMID:24771339 doi:http://dx.doi.org/10.1093/nar/gku330

See Also

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

Personal tools