User:Wayne Decatur/Structure analysis tools: Difference between revisions
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* [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]]. | ||
* [http://prody.csb.pitt.edu/index.html ProDy Project] - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files. | * [http://prody.csb.pitt.edu/index.html ProDy Project] - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files. | ||
* [https://proteins.plus/ ProteinsPlus] - a comprehensive collection of web-based molecular modeling tools. Associated [https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac305/6576358?login=false article]. | |||
==Nucleic acid in general== | ==Nucleic acid in general== | ||
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* 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. | ||
* [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." | |||
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* [https://github.com/fomightez/pdbsum-binder Collection of notebooks to analyze PDBsum-derived data using Jupyter/Python] - currently the most prominent feature here facilitates highlighting differences and similarities in protein-protein interaction of the same protein pairs in '''different''', related macromolecular complexes. For example, structures solved with different ligands or substrates or structures that share subsets of the same components. | * [https://github.com/fomightez/pdbsum-binder Collection of notebooks to analyze PDBsum-derived data using Jupyter/Python] - currently the most prominent feature here facilitates highlighting differences and similarities in protein-protein interaction of the same protein pairs in '''different''', related macromolecular complexes. For example, structures solved with different ligands or substrates or structures that share subsets of the same components. | ||
* [https://github.com/fomightez/structurework/tree/master/pdbsum_utilities PDBsum-utilities] - where I share my code to analyze PDBsum-derived data using Python. | * [https://github.com/fomightez/structurework/tree/master/pdbsum_utilities PDBsum-utilities] - where I share my code to analyze PDBsum-derived data using Python. | ||
==Compare Related Structures Protein-Protein or Protein-nucleic Interaction Pairs== | |||
* [https://github.com/fomightez/structurework/tree/master/PISA-utilities PDBePISA-utilities] - where I share my code to analyze PDBePISA-derived data using Python. | |||
==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. | ||
