User:Wayne Decatur/Structure analysis tools: Difference between revisions
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* [https://genomicscomputbiol.org/ojs3/GCB/article/view/48 SNPViz - Visualization of SNPs in proteins] | * [https://genomicscomputbiol.org/ojs3/GCB/article/view/48 SNPViz - Visualization of SNPs in proteins] | ||
===Missing Residues=== | |||
==Compare Related Structures== | ===Compare Related Structures Protein-Protein Interaction Pairs=== | ||
* [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 | * [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. | ||
==Python-based utilities== | ===Python-based utilities=== | ||
* 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. | ||
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* [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. | ||
- [ | - [https://github.com/fomightez/pdbsum-binder pdbsum-binder] - working with data from PDBsum integrated with Jupyter/Python | ||
- [ | - [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder] - JMol Jsmol applets in Jupyter notebook | ||
- [ | - [https://github.com/fomightez/Jupyter-desktop_with_pymol Jupyter-desktop_with_pymol] - PyMOL graphical user interface served via MyBinder.org | ||
- [ | - [https://github.com/fomightez/pymol-binder pymol-binder] - PyMOL running headless for command line/scripting and interaction with Python. | ||
- [ | - [https://github.com/fomightez/modelit-binder modelit-binder] - Model.it software to produce a 3D model of DNA in bent confirmation combined with Jupyter ecosystem and PyMOL served via MyBinder.org | ||
- [ | - [https://github.com/fomightez/AnimatePymolWithJmol AnimatePymolWithJmol] - Easily animate PyMOL session scenes with Jmol to create an animated GIFs | ||
==R-based utilities== | ===R-based utilities=== | ||
* [https://github.com/fomightez/bio3d-binder Bio3D (an R library) example along with Bio3D Python in same Jupyter notebook examples] | * [https://github.com/fomightez/bio3d-binder Bio3D (an R library) example along with Bio3D Python in same Jupyter notebook examples] | ||
==My own structure work-related code== | ===My own structure work-related code=== | ||
* [https://github.com/fomightez/structurework Structure/model manipulation Python code] | * [https://github.com/fomightez/structurework Structure/model manipulation Python code] | ||
* see also on [https://github.com/fomightez/structurework 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 | * see also on [https://github.com/fomightez/structurework 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 | ||
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* My [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | * My [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | ||
==Jmol/Jsmol use in Jupyter environments== | ===Jmol/Jsmol use in Jupyter environments=== | ||
* [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder] - My current resource consolidating my efforts to use Jsmol applets in Jupyter and to take advantage of a Jupyter extension made by others to also do that. Jsmol applets directly used in Jupyter are shown [https://nbviewer.jupyter.org/github/fomightez/jupyter-jsmol-binder/blob/master/Jmol%20Jsmol%20applets%20working%20in%20Jupyter%20notebooks.ipynb here]; you can run that notebook actively inside the [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder]. | * [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder] - My current resource consolidating my efforts to use Jsmol applets in Jupyter and to take advantage of a Jupyter extension made by others to also do that. Jsmol applets directly used in Jupyter are shown [https://nbviewer.jupyter.org/github/fomightez/jupyter-jsmol-binder/blob/master/Jmol%20Jsmol%20applets%20working%20in%20Jupyter%20notebooks.ipynb here]; you can run that notebook actively inside the [https://github.com/fomightez/jupyter-jsmol-binder jupyter-jsmol-binder]. | ||
===Related=== | |||
* [[User:Wayne Decatur/I-Ppo Morph Methods]] - uses several structure analysis tools to generate a [[morph]] of a protein-nucleic acid complex | |||
* [https://www.ebi.ac.uk/complexportal/complex/search?query=*&species=Saccharomyces%20cerevisiae%20(strain%20ATCC%20204508%20%2F%20S288c)&page=1 S. cerevisiae complexes] | |||
==References== | ==References== | ||
