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

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* [http://wishart.biology.ualberta.ca/SuperPose/ Superpose from the University of Alberta] -a protein superposition server.
* [http://wishart.biology.ualberta.ca/SuperPose/ Superpose from the University of Alberta] -a protein superposition server, see [https://proteopedia.org/wiki/index.php/Structural_alignment_tools#SuperPose|more detailed coverage on Proteopedia about SuperPose here in relation to other structural alignment tools/servers].
* [https://zhanglab.ccmb.med.umich.edu/TM-align/ TM-align] -a protein superposition/ structural alignment tool/server from the Zhang lab at the University of Michigan. "TM-align: Quick & Accurate Structural Alignment. TM-align is an algorithm for sequence independent protein structure comparisons. For two protein structures of unknown equivalence,...", see [https://proteopedia.org/wiki/index.php/Structural_alignment_tools#TM-Align|more detailed coverage on Proteopedia about TM-align here in relation to other structural alignment tools/servers].
* [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
* [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
* [http://ffas.burnham.org/XtalPred-cgi/xtal.pl XtalPred] - Prediction of Protein Crystallizability (program described by ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220968/ this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."]<ref>PMID:25372670 </ref>, supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.)
* [http://ffas.burnham.org/XtalPred-cgi/xtal.pl XtalPred] - Prediction of Protein Crystallizability (program described by ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220968/ this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."]<ref>PMID:25372670 </ref>, supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.)
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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==


* Curves+ is a revised version of the Curves approach for analyzing the structure of nucleic acids. The webserver form can be accessed [http://curvesplus.bsc.es/ here] where citations of the related articles are in another tab. There seems to be a command line-based one in Fortran available [https://bisi.ibcp.fr/tools/curves_plus/curves-user-guide.html here].
* Curves+ is a revised version of the Curves approach for analyzing the structure of nucleic acids. The webserver form can be accessed [http://curvesplus.bsc.es/ here] where citations of the related articles are in another tab. There seems to be a command line-based one in Fortran available [https://bisi.ibcp.fr/tools/curves_plus/curves-user-guide.html here].
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===RNA specific===
==RNA specific==


* [https://github.com/fjossinet/RNAGallery RNArtist RNA Gallery] - Precomputed 2-dimensional drawings for RNA structures stored in databases.
* [https://github.com/fjossinet/RNAGallery RNArtist RNA Gallery] - Precomputed 2-dimensional drawings for RNA structures stored in databases.
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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."




 
==Mutations==
===Mutations===


* [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===
==Missing Residues==


* [[FirstGlance_in_Jmol | FirstGlance in Jmol]] offers a detailed report on the numbers and properties of parts of chains not observed in a structure. Open your favorite molecule in FirstGlance in Jmol and then click on the 'Missing Residues' link on the first page that opens, under `Asymmetric Unit` section.
* [[FirstGlance_in_Jmol | FirstGlance in Jmol]] offers a detailed report on the numbers and properties of parts of chains not observed in a structure. Open your favorite molecule in FirstGlance in Jmol and then click on the 'Missing Residues' link on the first page that opens, under `Asymmetric Unit` section.
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* Missing strings of residues in protein crystal structures. Djinovic-Carugo K, Carugo O.Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.<ref>PMID: 28232893 </ref>
* Missing strings of residues in protein crystal structures. Djinovic-Carugo K, Carugo O.Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.<ref>PMID: 28232893 </ref>
* Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. DeForte S, Uversky VN.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. <ref>PMID: 26683124</ref>  
* Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. DeForte S, Uversky VN.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. <ref>PMID: 26683124</ref>  
* see 'Compare Related Structures in regards to portions not resolved' section below


===Compare Related Structures in regards to portions not resolved===
==Compare Related Structures in regards to portions not resolved==


** ''work-in-progress'' effort to make it easier to make summary tables of part of chains not resolved in '''related''' solved macromolecular complexes.
** ''work-in-progress'' effort to make it easier to make summary tables of part of chains not resolved in '''related''' solved macromolecular complexes.


===Compare Related Structures Protein-Protein Interaction Pairs===
==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 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.
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* [https://github.com/fomightez/AnimatePymolWithJmol AnimatePymolWithJmol] - Easily animate PyMOL session scenes with Jmol to create an animated GIFs
* [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
* click `launch binder` [https://github.com/fomightez/cl_demo-binder here] for a series of demonstrations of useful resources on command line for manipulating structure files.
* click `launch binder` [https://github.com/fomightez/cl_demo-binder here] for a series of demonstrations of useful resources on command line for manipulating structure files.
* see 'Compare Related Structures in regards to portions not resolved' section below
* 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===
==Related==
* [[User:Wayne Decatur/I-Ppo Morph Methods]] - uses several structure analysis tools to generate a [[morph]] of a protein-nucleic acid complex
* [[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]
* [https://www.ebi.ac.uk/complexportal/complex/search?query=*&species=Saccharomyces%20cerevisiae%20(strain%20ATCC%20204508%20%2F%20S288c)&page=1 S. cerevisiae complexes]
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