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 | * [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== | ||
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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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* 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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* [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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* 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. | ||
