User:Wayne Decatur
From Proteopedia
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Protopedia recognizes <br> and <p></p> but most times <p></p> not necessary. | Protopedia recognizes <br> and <p></p> but most times <p></p> not necessary. | ||
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| - | + | Research Associate in the Department of Biochemistry and Molecular Biology at the SUNY Upstate Medical University.<br> | |
'''Member of the [[Proteopedia:About#The Proteopedia Team|Proteopedia Editorial Board]]'''. | '''Member of the [[Proteopedia:About#The Proteopedia Team|Proteopedia Editorial Board]]'''. | ||
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<!--[http://people.umass.edu/wdecatur/index.html Wayne's site on the web] NO LONGER WORKS--> | <!--[http://people.umass.edu/wdecatur/index.html Wayne's site on the web] NO LONGER WORKS--> | ||
| - | [http://www.unh.edu/biochemistry/sower/post-doc-wayne-decatur.html Wayne's page on the Sower Lab site] | + | <!--[http://www.unh.edu/biochemistry/sower/post-doc-wayne-decatur.html Wayne's page on the Sower Lab site]--> |
| + | |||
| + | [http://fomightez.github.io/ Wayne at Github] | ||
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=PubMed&term=%22decatur-wa%22%5bau%5d Wayne's publications listed at the the U.S. National Library of Medicine's PubMed database] | [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=PubMed&term=%22decatur-wa%22%5bau%5d Wayne's publications listed at the the U.S. National Library of Medicine's PubMed database] | ||
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*[[Flock house virus B2 protein Suppression of RNA Silencing]] | *[[Flock house virus B2 protein Suppression of RNA Silencing]] | ||
*[[Green Fluorescent Protein]] | *[[Green Fluorescent Protein]] | ||
| - | *[[ | + | *[[Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa|DEAD-box helicase protein Vasa]] |
| - | *[[3dmq|Swi2/Snf2 protein RapA]] | + | <!--*[[3dmq|Swi2/Snf2 protein RapA]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! ---> |
| - | *[[2eyq|Mfd (TRCF, transcription-repair coupling factor)]] | + | <!--*[[2eyq|Mfd (TRCF, transcription-repair coupling factor)]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! ---> |
| - | *[[3fpn|UvrA-UvrB interaction domains complex]] | + | <!--*[[3fpn|UvrA-UvrB interaction domains complex]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! ---> |
| - | *[[3ews|DExD/H-box RNA-dependent ATPase DDX19 in the open]] and [[3g0h|closed]] cleft conformation | + | <!--*[[3ews|DExD/H-box RNA-dependent ATPase DDX19 in the open]] and [[3g0h|closed]] cleft conformation I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! ---> |
| - | *[[3gfp|C-terminal domain of the DExD/H-box RNA-dependent ATPase Dbp5]] | + | <!--*[[3gfp|C-terminal domain of the DExD/H-box RNA-dependent ATPase Dbp5]]| I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! ---> |
| - | *[[ | + | *[[RecG Bound to Three-Way DNA Junction|RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork]] |
| - | *[[ | + | *[[LepA|Escherichia coli LepA, the ribosomal back translocase]] |
| - | *[[Pore forming toxin, α- | + | *[[Pore forming toxin, α-hemolysin|The Pore Forming Toxin, α-hemolysin]] |
| - | *[[3lqq|CED-4 Apoptosome]] | + | <!--*[[3lqq|CED-4 Apoptosome]] SEEMS EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! I DID FInd the FILE FOR THE MORPH FOR THIS PAGE LISTED IN MY USER CONTRIBUTIONS--> |
*[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]] | *[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]] | ||
*[[Luciferase]] | *[[Luciferase]] | ||
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*[[Leucine-rich repeat|Leucine-Rich Repeat Proteins]] | *[[Leucine-rich repeat|Leucine-Rich Repeat Proteins]] | ||
*[[Toll-like Receptors]] | *[[Toll-like Receptors]] | ||
| + | *[[Hormone]] | ||
*[[Human Follicle-Stimulating Hormone Complexed with its Receptor]] | *[[Human Follicle-Stimulating Hormone Complexed with its Receptor]] | ||
| + | *[[G protein-coupled receptor]] | ||
*[[Forkhead box protein M1]] | *[[Forkhead box protein M1]] | ||
| - | <!--*[[2beg|amyloid-beta fibrils]]--> | + | <!--*[[2beg|amyloid-beta fibrils]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! WOULD NEED TO MOVE TO BETTER NAMED PAGE ---> |
| + | *[[Kink-turn motif]] | ||
| + | *[[Pseudouridine]] | ||
| + | *[[Zika virus subgenomic flaviviral RNA]] | ||
| + | *[[RNase P]] | ||
| + | *[[yeast RNase P]] | ||
| + | *[[Cubic Diamond Lattice Metal-Organic Framework]] | ||
| + | *[[Catalytic Molybdenum Metal-Organic Framework]] | ||
===Topic Pages - Structural Bioinformatics=== | ===Topic Pages - Structural Bioinformatics=== | ||
*[[About Macromolecular Structure]] | *[[About Macromolecular Structure]] | ||
| + | *[[Alternate locations]] | ||
| + | *[[altloc]] | ||
*[[Cation-pi interactions]] | *[[Cation-pi interactions]] | ||
| + | *[[Complexes]] | ||
*[[Cystine]] | *[[Cystine]] | ||
*[[Getting Unremediated PDB Files]] | *[[Getting Unremediated PDB Files]] | ||
*[[Net charge]] | *[[Net charge]] | ||
| + | *[[Pseudoenzyme]] | ||
| + | *[[Interface analysis servers]] | ||
*[[Isoelectric point]] | *[[Isoelectric point]] | ||
*[[Standard Residues]] and [[Non-Standard Residues]] | *[[Standard Residues]] and [[Non-Standard Residues]] | ||
| + | *[[Web servers for convenient generation of publication-quality figures for molecular views]] | ||
===Topic Pages - Education=== | ===Topic Pages - Education=== | ||
| - | *[[Teaching Strategies Using Proteopedia]] | + | * [[Teaching Strategies Using Proteopedia]] |
| - | *[[Teaching Scenes, Tutorials, and Educators' Pages]] | + | * [[Teaching Scenes, Tutorials, and Educators' Pages]] |
| - | *[[High school teachers' resources]] | + | * [[Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching]] |
| + | ** ''Link above is the online version of Part C of a book chapter entitled '''Publishing in Proteopedia: The Guide''' by [[User:Jaime Prilusky|Jaime Prilusky]], [[User:Wayne Decatur|Wayne Decatur]], and [[User:Eric Martz|Eric Martz]]." | ||
| + | **'''Full Reference''': ''Jaime Prilusky, Wayne Decatur, Eric Martz. Publishing in Proteopedia: The Guide, Advancing Methods for Biomolecular Crystallography. ''In'' NATO Science for Peace and Security Series A: Chemistry and Biology 2013, pp 277-295 [[http://dx.doi.org/10.1007/978-94-007-6232-9_24 doi:10.1007/978-94-007-6232-9_24]]'' | ||
| + | * [[High school teachers' resources]] | ||
===Meta Pages=== | ===Meta Pages=== | ||
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* [[Proteopedia:Facebook]] | * [[Proteopedia:Facebook]] | ||
* [[Proteopedia:Twitter]] | * [[Proteopedia:Twitter]] | ||
| + | * [[Proteopedia:Macros]] | ||
| + | * [[Proteopedia:DIY:Macros]] | ||
| + | * [[Proteopedia:Cookbook]] | ||
| + | * [[Combine Proteopedia scenes with inline JSmol scripting]] | ||
| + | * [[Proteopedia:DIY:Templates]] | ||
* [[Jmol]] | * [[Jmol]] | ||
* [[DRuMS]] | * [[DRuMS]] | ||
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* [[Pages needing improvement]] | * [[Pages needing improvement]] | ||
| - | ==Workshops and Seminars== | + | ==Workshops, Lectures, and Seminars== |
| + | *[[User:Wayne Decatur/ GS647-021 Structuring against Coronavirus 2020| UPSTATE MEDICAL GS647-021 Nanocourse: Structuring against Coronavirus (April-May) 2020]] | ||
| + | *[[User:Wayne Decatur/UNH BCHEM833 Structural Analysis Workshop Session Fall 2012|UNH BIOCHEM833 Structural Analysis for Non-Structural Biologists Workshop Session Fall Semester (November 8th) 2012]] | ||
| + | *[[User:Wayne Decatur/UNH BCHEM833 Structural Proteomics Introductory Lecture Fall 2012|UNH BIOCHEM833 Structural Analysis for Non-Structural Biologists Introductory Lecture Fall Semester (October 25th) 2012]] | ||
*[[User:Wayne Decatur/NASCE2011|Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011]] | *[[User:Wayne Decatur/NASCE2011|Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011]] | ||
*[[User:Wayne Decatur/UNH CME Workshop March 11 2011|Workshop for CME at the University of New Hampshire, Durham, NH March 11 2011]] | *[[User:Wayne Decatur/UNH CME Workshop March 11 2011|Workshop for CME at the University of New Hampshire, Durham, NH March 11 2011]] | ||
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*[[Sandbox1rpu]] working out configuration&isosurfaces&dots problems | *[[Sandbox1rpu]] working out configuration&isosurfaces&dots problems | ||
*[[Sandbox2hvy]] test for dots in another file | *[[Sandbox2hvy]] test for dots in another file | ||
| - | * [[Sandbox3pla]] | ||
* [[Sandbox CsrA]] | * [[Sandbox CsrA]] | ||
| - | * [[Sandbox | + | * [[Sandbox TestMultiSurface]] |
===Protected Sandbox Pages=== | ===Protected Sandbox Pages=== | ||
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*[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]] | *[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]] | ||
*[[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]] | *[[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]] | ||
| - | *[[User: | + | *[[User:Wayne Decatur/kink-turn motif]] |
*[[User:Wayne Decatur/Teaching Proteopedia]] | *[[User:Wayne Decatur/Teaching Proteopedia]] | ||
*[[User:Wayne Decatur/Editing Getting Unremediated PDB Files]] | *[[User:Wayne Decatur/Editing Getting Unremediated PDB Files]] | ||
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*[[User:Wayne Decatur/Generate Unfolded Structures]] | *[[User:Wayne Decatur/Generate Unfolded Structures]] | ||
*[[User:Wayne Decatur/Alter Disulfide Bonds in a Structure ]] | *[[User:Wayne Decatur/Alter Disulfide Bonds in a Structure ]] | ||
| + | *[[User:Wayne Decatur/4ay9 pymol]] | ||
| + | *[[User:Wayne Decatur/Gal 4]] | ||
| + | *[[User:Wayne Decatur/mof_dev]] | ||
*[[User:Wayne Decatur/Homology Modeling]] | *[[User:Wayne Decatur/Homology Modeling]] | ||
*[[User:Wayne Decatur/Sequence analysis tools]] | *[[User:Wayne Decatur/Sequence analysis tools]] | ||
| + | *[[User:Wayne Decatur/Structure analysis tools]] | ||
*[[User:Wayne Decatur/Molecular modeling tools]] | *[[User:Wayne Decatur/Molecular modeling tools]] | ||
*[[User:Wayne Decatur/BioWikis]] | *[[User:Wayne Decatur/BioWikis]] | ||
| + | *[[User:Wayne Decatur/Code for Molecular Structure and Visualization Work]] | ||
*[[User:Wayne Decatur/I-Ppo Morph Methods]] | *[[User:Wayne Decatur/I-Ppo Morph Methods]] | ||
*[[User:Wayne Decatur/3kg2 Morph Methods]] | *[[User:Wayne Decatur/3kg2 Morph Methods]] | ||
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*[[User:Wayne Decatur/humanaGal3hg2toothers morph methods]] | *[[User:Wayne Decatur/humanaGal3hg2toothers morph methods]] | ||
*[[User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods]] | *[[User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods]] | ||
| + | *[[User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods]] | ||
| + | *[[User:Wayne Decatur/Converting Exported Proteopedia Pages from Jmol to JSmol]] | ||
===Templates=== | ===Templates=== | ||
Current revision
Contents |
Wayne Decatur
Research Associate in the Department of Biochemistry and Molecular Biology at the SUNY Upstate Medical University.
Member of the Proteopedia Editorial Board.
Interests:
small RNAs and their associated ribonucleoprotein complexes; the Ribosome; RNA modification; catalytic RNAs; homing endonucleases, group I introns; leucine-rich repeats; hormones and their receptors.
Wayne's publications listed at the the U.S. National Library of Medicine's PubMed database
email: 
Some Proteopedia Pages to Which I've Contributed
Molecules: Topic Pages
- The Ribosome
- Large Ribosomal Subunit of Haloarcula marismortui
- Interactions between Antibiotics and the Ribosome
- Azithromycin bound to the Large Ribosomal Subunit of Haloarcula marismortui
- Suppression of RNA Silencing by Viruses
- Plant Viral Protein p19 Suppression of RNA Silencing
- Tomato aspermy virus protein 2b Suppression of RNA Silencing
- Flock house virus B2 protein Suppression of RNA Silencing
- Green Fluorescent Protein
- DEAD-box helicase protein Vasa
- RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork
- Escherichia coli LepA, the ribosomal back translocase
- The Pore Forming Toxin, α-hemolysin
- The Glutamate Receptor (GluA2)
- Luciferase
- Citrate Synthase
- Lamprey Variable Lymphocyte Receptor
- Leucine-Rich Repeat Proteins
- Toll-like Receptors
- Hormone
- Human Follicle-Stimulating Hormone Complexed with its Receptor
- G protein-coupled receptor
- Forkhead box protein M1
- Kink-turn motif
- Pseudouridine
- Zika virus subgenomic flaviviral RNA
- RNase P
- yeast RNase P
- Cubic Diamond Lattice Metal-Organic Framework
- Catalytic Molybdenum Metal-Organic Framework
Topic Pages - Structural Bioinformatics
- About Macromolecular Structure
- Alternate locations
- altloc
- Cation-pi interactions
- Complexes
- Cystine
- Getting Unremediated PDB Files
- Net charge
- Pseudoenzyme
- Interface analysis servers
- Isoelectric point
- Standard Residues and Non-Standard Residues
- Web servers for convenient generation of publication-quality figures for molecular views
Topic Pages - Education
- Teaching Strategies Using Proteopedia
- Teaching Scenes, Tutorials, and Educators' Pages
- Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching
- Link above is the online version of Part C of a book chapter entitled Publishing in Proteopedia: The Guide by Jaime Prilusky, Wayne Decatur, and Eric Martz."
- Full Reference: Jaime Prilusky, Wayne Decatur, Eric Martz. Publishing in Proteopedia: The Guide, Advancing Methods for Biomolecular Crystallography. In NATO Science for Peace and Security Series A: Chemistry and Biology 2013, pp 277-295 [doi:10.1007/978-94-007-6232-9_24]
- High school teachers' resources
Meta Pages
- Help:Editing
- Proteopedia:How to Make a Page
- Proteopedia:About
- Proteopedia:Policy
- Proteopedia:Facebook
- Proteopedia:Twitter
- Proteopedia:Macros
- Proteopedia:DIY:Macros
- Proteopedia:Cookbook
- Combine Proteopedia scenes with inline JSmol scripting
- Proteopedia:DIY:Templates
- Jmol
- DRuMS
- Wanted pages
- Pages needing expansion
- Pages needing improvement
Workshops, Lectures, and Seminars
- UPSTATE MEDICAL GS647-021 Nanocourse: Structuring against Coronavirus (April-May) 2020
- UNH BIOCHEM833 Structural Analysis for Non-Structural Biologists Workshop Session Fall Semester (November 8th) 2012
- UNH BIOCHEM833 Structural Analysis for Non-Structural Biologists Introductory Lecture Fall Semester (October 25th) 2012
- Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011
- Workshop for CME at the University of New Hampshire, Durham, NH March 11 2011
- Seminar at the University of New Hampshire, Durham, NH Feb 1st 2011
- Biochem642 Molecular Visualization 2010 Fall Sessions
- Biochem642 Molecular Visualization 2009 Fall Sessions
- Proteopedia Work Session for Chem 791A-Biomolecular Structure
Personal Quicklinks
All Protected Pages
Files Uploaded
Sandboxes
- Sandbox1rpu working out configuration&isosurfaces&dots problems
- Sandbox2hvy test for dots in another file
- Sandbox CsrA
- Sandbox TestMultiSurface
Protected Sandbox Pages
Protected Topic Pages
- User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit
- User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin
- User:Wayne Decatur/Interactions between Antibiotics and the Ribosome
- User:Wayne Decatur/Suppression of RNA Silencing by Viruses
- User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing
- User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing
- User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing
- User:Wayne Decatur/kink-turn motif
- User:Wayne Decatur/Teaching Proteopedia
- User:Wayne Decatur/Editing Getting Unremediated PDB Files
- User:Wayne Decatur/Moving Components or Parts of Structures
- User:Wayne Decatur/Generate Unfolded Structures
- User:Wayne Decatur/Alter Disulfide Bonds in a Structure
- User:Wayne Decatur/4ay9 pymol
- User:Wayne Decatur/Gal 4
- User:Wayne Decatur/mof_dev
- User:Wayne Decatur/Homology Modeling
- User:Wayne Decatur/Sequence analysis tools
- User:Wayne Decatur/Structure analysis tools
- User:Wayne Decatur/Molecular modeling tools
- User:Wayne Decatur/BioWikis
- User:Wayne Decatur/Code for Molecular Structure and Visualization Work
- User:Wayne Decatur/I-Ppo Morph Methods
- User:Wayne Decatur/3kg2 Morph Methods
- User:Wayne Decatur/3fpn Morph methods
- User:Wayne Decatur/3ewsSLASH3g0h Morph methods
- User:Wayne Decatur/humanaGal3hg2toothers morph methods
- User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods
- User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods
- User:Wayne Decatur/Converting Exported Proteopedia Pages from Jmol to JSmol
Templates
Help
- Proteopedia:Problems
- Jmol Command Reference Manual for advanced scene authoring.
- Jmol Wiki
Useful Resources
Wikitext help
- URLS in external links has the codes for using characters that aren't A-Z a-z 0-9 ._\/~%-+&#?!=()@ in links
- Guide to Wikitext Markup Language (wiki code)
- How to edit illustrates use of nowiki and pre tags.
- Wikitext quick cheat sheet also has how to make link to categories, too
- Categories can be linked to with colon in front
- HTML in wikitext
- Allows cropping of images, in addition to annotating.
- WikiTable Markup Guide
- Editing Wikitext/Tables
- Images: linking to articles using wikitext
