User:Wayne Decatur/Structure analysis tools - Revision history

Wayne Decatur: add Gemmi

2023-02-22T17:30:59Z

add Gemmi

← Older revision		Revision as of 17:30, 22 February 2023
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	==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.

Wayne Decatur: fix link

2022-05-04T20:15:00Z

fix link

← Older revision		Revision as of 20:15, 4 May 2022
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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.
	* [~~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."

Wayne Decatur: add proteinsplus and rna-tools online

2022-05-04T20:14:10Z

add proteinsplus and rna-tools online

← Older revision		Revision as of 20:14, 4 May 2022
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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.
			* [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."


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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.

Wayne Decatur: add links in other sections

2021-03-26T14:31:34Z

add links in other sections

← Older revision		Revision as of 14:31, 26 March 2021
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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==
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	* 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.

Wayne Decatur: add links to better coverage

2021-03-26T14:28:42Z

add links to better coverage

← Older revision		Revision as of 14:28, 26 March 2021
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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~~ 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,..."		* [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.)

Wayne Decatur: add TM-align

2021-03-26T14:19:34Z

add TM-align

← Older revision		Revision as of 14:19, 26 March 2021
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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.
			* [https://zhanglab.ccmb.med.umich.edu/TM-align/ TM-align] -a protein superposition/ structural alignment tool/server from 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,..."
	* [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.)

Wayne Decatur: make consistent headers

2021-01-11T19:24:31Z

make consistent headers

← Older revision		Revision as of 19:24, 11 January 2021
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	* [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.

	===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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	===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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	* 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>

	===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.
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	===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]].
	* 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.
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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
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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===		==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]

Wayne Decatur at 19:18, 11 January 2021

2021-01-11T19:18:14Z

← Older revision		Revision as of 19:18, 11 January 2021
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	===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]].
	* 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.

Wayne Decatur: fix wikitext of new additions

2021-01-11T19:17:09Z

fix wikitext of new additions

← Older revision		Revision as of 19:17, 11 January 2021
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	* article associated with it: [https://academic.oup.com/nar/article/36/suppl_2/W255/2506064 SEQATOMS] Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/		* article associated with it: [https://academic.oup.com/nar/article/36/suppl_2/W255/2506064 SEQATOMS] Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
	* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16. <ref>PMID: 25559128</ref> <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).		* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16. <ref>PMID: 25559128</ref> <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).
	* Missing strings of residues in protein crystal structures.		* 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>
	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>

Wayne Decatur: fix wikitext

2021-01-11T19:16:04Z

fix wikitext

← Older revision		Revision as of 19:16, 11 January 2021
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	* [[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.
	* Biopython can use REMARK 465 lines to parse missing residues, see my notebook `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo] ( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]). Also see [https://github.com/biopython/biopython/pull/1237 here] and [https://github.com/biopython/biopython/issues/3306 here].		* Biopython can use REMARK 465 lines to parse missing residues, see my notebook `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo] ( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]). Also see [https://github.com/biopython/biopython/pull/1237 here] and [https://github.com/biopython/biopython/issues/3306 here].
	* article associated with it:		* article associated with it: [https://academic.oup.com/nar/article/36/suppl_2/W255/2506064 SEQATOMS] Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
	[~~SEQATOMS: a web tool for identifying missing regions in PDB in sequence context](~~https://academic.oup.com/nar/article/36/suppl_2/W255/2506064)		* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16. <ref>PMID: 25559128</ref> <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).
	Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
	* MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.
	He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.
	BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16.
	PMID: 25559128 <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my [https://github.com/fomightez/cl_demo-binder cl_demo-binder repo]( [https://nbviewer.jupyter.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Using%20Biopython%20PDB%20Header%20Parser%20to%20get%20missing%20residues.ipynb nicely rendered static version of that notebook]).
	* Missing strings of residues in protein crystal structures.		* 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>		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>