View source for User:Wayne Decatur/Structure analysis tools

* [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.
* [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.)
* [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer]
* [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.
* [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==

* 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].

* Despite what the name original stood for, DSSR handles nucleic acids in general as well. See the description below for links.


==RNA specific==

* [https://github.com/fjossinet/RNAGallery RNArtist RNA Gallery] - Precomputed 2-dimensional drawings for RNA structures stored in databases.
* DSSR -(Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. [http://www.ncbi.nlm.nih.gov/pubmed/?term=DSSR%3A+an+integrated+software+tool+for+dissecting+the+spatial+structure+of+RNA PMID: 26184874 ]<ref>PMID: 26184874</ref>  (Maybe name of given supplemental data file previously DSSR stood for "DSSR_ a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates".? [[Jmol]] now has integrated real time updates to data generated by DSSR, see [https://www.google.com/search?q=jmol+dssr&oq=jmol+dssr&aqs=chrome.0.69i59j69i60.4221j0j7&sourceid=chrome&es_sm=91&ie=UTF-8 here] and [https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365 a 2017 article on it here]<ref>PMID: 28472503</ref>.
* 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://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==

* [https://genomicscomputbiol.org/ojs3/GCB/article/view/48 SNPViz - Visualization of SNPs in proteins]


==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.
* 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: [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]). 
* 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> 
* see 'Compare Related Structures in regards to portions not resolved' section below

==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.

==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/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==
* [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.
* [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.
* 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.
* [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==

* [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==
* [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
* 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.

==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].

==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==
{{Reflist}}

==See Also==
* [[Structural alignment tools]]
* [[User:Wayne Decatur/Molecular modeling tools|Modeling]]
* [[Molecular modeling and visualization software]]
* [[User:Wayne Decatur/Code for Molecular Structure and Visualization Work]]