User:Wayne Decatur/Structure analysis tools: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
add proteinsplus and rna-tools online
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
add Gemmi
 
(One intermediate revision by the same user not shown)
Line 21: Line 21:
* RNApdbee -a webserver to derive secondary structures from PDB files of knotted and unknotted RNAs [http://www.ncbi.nlm.nih.gov/pubmed/24771339 PMID: 24771339]<ref>PMID: 24771339</ref>. Use it [http://rnapdbee.cs.put.poznan.pl/ here].
* RNApdbee -a webserver to derive secondary structures from PDB files of knotted and unknotted RNAs [http://www.ncbi.nlm.nih.gov/pubmed/24771339 PMID: 24771339]<ref>PMID: 24771339</ref>. Use it [http://rnapdbee.cs.put.poznan.pl/ here].
* [https://github.com/fjossinet/RNArtist RNArtist] -  allows designing of RNA 2D structures interactively. To help you to be an RNArtist, this tool provides numerous graphical options to find your theme and to modify the 2D layout.
* [https://github.com/fjossinet/RNArtist RNArtist] -  allows designing of RNA 2D structures interactively. To help you to be an RNArtist, this tool provides numerous graphical options to find your theme and to modify the 2D layout.
* [RNA-tools https://rna-tools.online/] - "rna-tools is a core library and a set of programs to run various Python functions related to work, initially, with PDB files of RNA structures, but right now this is a huge toolbox of tools to process various types of RNA data."
* [https://rna-tools.online/ RNA-tools] - "rna-tools is a core library and a set of programs to run various Python functions related to work, initially, with PDB files of RNA structures, but right now this is a huge toolbox of tools to process various types of RNA data."




Line 54: Line 54:
==Python-based utilities==
==Python-based utilities==
* [http://rasbt.github.io/biopandas/  BioPandas] - "Working with molecular structures in pandas DataFrames". Combining Python, Pandas, and Structural data awesomely. Has nice PDB parser that lets you get whole header, for example see [[http://rasbt.github.io/biopandas/tutorials/Working_with_PDB_Structures_in_DataFrames/ here]].
* [http://rasbt.github.io/biopandas/  BioPandas] - "Working with molecular structures in pandas DataFrames". Combining Python, Pandas, and Structural data awesomely. Has nice PDB parser that lets you get whole header, for example see [[http://rasbt.github.io/biopandas/tutorials/Working_with_PDB_Structures_in_DataFrames/ here]].
* [https://gemmi.readthedocs.io/en/latest/index.html Gemmi] - is a library for  parsing PDB, cif, mtz files, and has Python bindings
* Use PyMOL via the command line in your browser in a Jupyter session by clicking `launch binder` [https://github.com/fomightez/pymol-binder here].  A series of demonstrations of using PyMOL in the manner are included.
* Use PyMOL via the command line in your browser in a Jupyter session by clicking `launch binder` [https://github.com/fomightez/pymol-binder here].  A series of demonstrations of using PyMOL in the manner are included.
* [https://github.com/fhcrc/seqmagick 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.
* [https://github.com/fhcrc/seqmagick 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.
Retrieved from "https://proteopedia.org/User:Wayne_Decatur/Structure_analysis_tools"