User:Wayne Decatur

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Research Associate in the Department of Biochemistry and Molecular Biology at the University of Massachusetts at Amherst.
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[[Image:Me cropped smaller at Eileen Jewel performance 11-9-08..jpg|right|300px|Wayne Decatur in front row of Eilen Jewel private performance November 9th, 2008 at Williamsburg, MA Grange Hall]]<br />
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==Wayne Decatur==
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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>
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'''Member of the [[Proteopedia:About#The Proteopedia Team|Proteopedia Editorial Board]]'''.
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Interests:
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<p>
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small RNAs and their associated ribonucleprotein complexes; the Ribosome; catalytic RNAs; homing endonucleases
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Interests:<br>
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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.
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</p>
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==Personal Quicklinks==
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<!--[http://people.umass.edu/wdecatur/index.html Wayne's site on the web] NO LONGER WORKS-->
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===All Protected Pages===
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<!--[http://www.unh.edu/biochemistry/sower/post-doc-wayne-decatur.html Wayne's page on the Sower Lab site]-->
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*[http://proteopedia.org/wiki/index.php?title=Special:Contributions&limit=500&contribs=user&target=Wayne+Decatur&namespace=2 Search for User:Wayne Decatur in User Namespace]
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===Files Uploaded===
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[http://fomightez.github.io/ Wayne at Github]
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*[http://proteopedia.org/wiki/index.php?limit=100&title=Special%3AContributions&contribs=user&target=Wayne+Decatur&namespace=6&year=&month=-1 Files Uploaded by Wayne Decatur]
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[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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==Two Types of "Impact"==
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email: {{Template:Decatur_email}}
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Macromolecular 3D structures can impact '''scientific understanding''' and/or '''save lives''' by contributing to [[Structure-based drug design]]. The first list below, [[#Highest Impact Macromolecular Structures of All Time|Highest Impact Macromolecular Structures of All Time]], concerns impact on scientific understanding. A separate list below concerns [[#Structures Saving The Most Lives|Structures Saving The Most Lives]].
 
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==Highest Impact Macromolecular Structures of All Time==
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==Some Proteopedia Pages to Which I've Contributed==
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===Molecules: Topic Pages===
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*[[Ribosome|The Ribosome]]
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*[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula marismortui]]
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*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]]
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*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|Azithromycin bound to the Large Ribosomal Subunit of Haloarcula marismortui]]
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*[[Suppression of RNA Silencing by Viruses]]
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*[[Plant Viral Protein p19 Suppression of RNA Silencing]]
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*[[Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
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*[[Flock house virus B2 protein Suppression of RNA Silencing]]
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*[[Green Fluorescent Protein]]
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*[[Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa|DEAD-box helicase protein Vasa]]
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<!--*[[3dmq|Swi2/Snf2 protein RapA]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! --->
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<!--*[[2eyq|Mfd (TRCF, transcription-repair coupling factor)]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! --->
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<!--*[[3fpn|UvrA-UvrB interaction domains complex]] I FEAR EVEN HISTORY WIPED OUT WHEN REPLACED PDB ID CONTENT WITH OCA?!?!! --->
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<!--*[[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?!?!! --->
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<!--*[[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?!?!! --->
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*[[RecG Bound to Three-Way DNA Junction|RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork]]
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*[[LepA|Escherichia coli LepA, the ribosomal back translocase]]
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*[[Pore forming toxin, α-hemolysin|The Pore Forming Toxin, &#945;-hemolysin]]
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<!--*[[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-->
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*[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]]
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*[[Luciferase]]
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*[[Citrate Synthase]]
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*[[Lamprey Variable Lymphocyte Receptor]]
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*[[Leucine-rich repeat|Leucine-Rich Repeat Proteins]]
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*[[Toll-like Receptors]]
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*[[Hormone]]
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*[[Human Follicle-Stimulating Hormone Complexed with its Receptor]]
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*[[G protein-coupled receptor]]
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*[[Forkhead box protein M1]]
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<!--*[[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 --->
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*[[Kink-turn motif]]
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*[[Pseudouridine]]
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*[[Zika virus subgenomic flaviviral RNA]]
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*[[RNase P]]
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*[[yeast RNase P]]
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Below you are invited to list pages about structures that you believe to be among the highest impact since the first empirical macromolecular structures were determined. Please do '''not''' list a structure unless you ''provide a justification in the form of a brief description of its impact''.
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===Topic Pages - Structural Bioinformatics===
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*[[About Macromolecular Structure]]
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*[[Alternate locations]]
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*[[altloc]]
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*[[Cation-pi interactions]]
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*[[Complexes]]
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*[[Cystine]]
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*[[Getting Unremediated PDB Files]]
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*[[Net charge]]
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*[[Pseudoenzyme]]
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*[[Interface analysis servers]]
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*[[Isoelectric point]]
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*[[Standard Residues]] and [[Non-Standard Residues]]
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*[[Web servers for convenient generation of publication-quality figures for molecular views]]
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More about some of the earliest structures and their PDB files is [http://www.umass.edu/microbio/rasmol/1st_xtls.htm here].
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===Topic Pages - Education===
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* [[Teaching Strategies Using Proteopedia]]
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* [[Teaching Scenes, Tutorials, and Educators' Pages]]
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* [[Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching]]
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** ''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]]."
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**'''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]]''
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* [[High school teachers' resources]]
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This list is in chronological order.
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===Meta Pages===
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* [[Help:Editing]]
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* [[Proteopedia:How to Make a Page]]
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* [[Proteopedia:About]]
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* [[Proteopedia:Policy]]
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* [[Proteopedia:Facebook]]
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* [[Proteopedia:Twitter]]
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* [[Proteopedia:Macros]]
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* [[Proteopedia:DIY:Macros]]
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* [[Proteopedia:Cookbook]]
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* [[Combine Proteopedia scenes with inline JSmol scripting]]
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* [[Proteopedia:DIY:Templates]]
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* [[Jmol]]
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* [[DRuMS]]
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* [[Wanted pages]]
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* [[Pages needing expansion‎]]
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* [[Pages needing improvement‎]]
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* '''1953 - DNA double helix''' (B form): Although Watson and Crick's model was theoretical, it was essentially correct, and for the first time explained the ability of genes to be faithfully copied during cell division. It was not confirmed by atomic resolution X-ray crystallography until 1973, using RNA dinucleotide crystals. A full turn of B form DNA was not solved until 1980 (cf. [[1bna]]), 27 years after Watson and Crick's model. More: click on DNA at the [http://atlas.molviz.org Atlas of Macromolecules]
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==Workshops, Lectures, and Seminars==
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*[[User:Wayne Decatur/ GS647-021 Structuring against Coronavirus 2020| UPSTATE MEDICAL GS647-021 Nanocourse: Structuring against Coronavirus (April-May) 2020]]
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*[[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]]
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*[[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]]
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*[[User:Wayne Decatur/NASCE2011|Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011]]
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*[[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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*[[User:Wayne Decatur/UNH Seminar Feb 1st 2011|Seminar at the University of New Hampshire, Durham, NH Feb 1st 2011]]
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*[[User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions|Biochem642 Molecular Visualization 2010 Fall Sessions]]
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*[[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions|Biochem642 Molecular Visualization 2009 Fall Sessions]]
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*[[User:Wayne Decatur/Chem791A Work Session|Proteopedia Work Session for Chem 791A-Biomolecular Structure]]
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* '''1958 - Myoglobin''': As the first protein structure that was determined, it is hard to exaggerate its impact. Before this structure, there was very little understanding of 3D protein structure.
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==Personal Quicklinks==
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* '''1965 - Lysozyme''': The first enzyme solved. ''Someone please elaborate on its impact.''
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===All Protected Pages===
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*[http://proteopedia.org/wiki/index.php?title=Special:Contributions&limit=500&contribs=user&target=Wayne+Decatur&namespace=2 Search for User:Wayne Decatur in User Namespace]
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* '''1970 - Deoxy-hemoglobin''': M. Perutz' second hemoglobin structure proved to be at least as important as the first, published two years earlier, as it demonstrated that a protein can have several conformations, and that its physiological role depends on how it changes from one to the other.
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===Files Uploaded===
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*[http://proteopedia.org/wiki/index.php?limit=100&title=Special%3AContributions&contribs=user&target=Wayne+Decatur&namespace=6&year=&month=-1 Files Uploaded by Wayne Decatur]
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* '''1974 - Transfer RNA''': The first 3D RNA structure solved. ''Someone please elaborate on its impact.''
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* '''1978 - Tobacco bushy stunt virus''': S. Harrison offered the first atomic scale image of a complete biological object, a plant virus. It was a technical feat, and revealed rules of architecture that, a few years later (1985), were shown to apply to human pathogens such as the common cold and the poliomyelitis viruses.
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* '''1987 - [[Major_Histocompatibility_Complex_Class_I | Major histocompatibility complex class I]]''': Created a paradigm shift in cellular immunology by explaining how MHC is involved in presenting hidden intracellular proteins to T lymphocytes. During the decade prior to this structure, this was a constantly debated but very murky mystery.
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* '''2000(?) - Ribosome''': This structure surprised almost everyone by showing that peptidyl transferase is a ribozyme, rather than a protein enzyme.
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==Structures Saving The Most Lives==
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Structures of the following molecules were used in [[Structure-based drug design|structure-based drug design]], and the resulting drugs have saved large numbers of lives.
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* [[Avian Influenza Neuraminidase, Tamiflu and Relenza|Influenza virus neuraminidase structure]] was used in designing the neuraminidase inhibitors [[Avian Influenza Neuraminidase, Tamiflu and Relenza|oseltamivir (Tamiflu&reg;) and zanamivir (Relenza&reg;)]]. Roche, the manufacturer of Tamiflu, estimates that 50 million people have been treated with this drug<ref>[http://www.roche.com/med-cor-2007-04-26 Roche update on Tamiflu for pandemic influenza preparedness], Media Release, April 26, 2007.</ref>. The [http://en.wikipedia.org/wiki/Cochrane_Collaboration Cochrane Collaboration] concluded that neuriminidase inhibitors "are effective in preventing and treating the symptoms and complications of influenza"<ref>[http://mrw.interscience.wiley.com/cochrane/clsysrev/articles/CD001265/frame.html Neuraminidase inhibitors for preventing and treating influenza in healthy adults], T. Jefferson ''et al.'', Cochrane Database of Systematic Reviews, Issue 4, 2008. DOI [http://dx.doi.org/10.1002/14651858.CD001265.pub2 10.1002/14651858.CD001265.pub2]</ref>. Influenza kills hundreds of thousands of people annually<ref>[http://en.wikipedia.org/wiki/Influenza Influenza] in Wikipedia.</ref>, including 40,000 in the United States<ref>[http://aje.oxfordjournals.org/cgi/content/full/163/2/181 Mortality due to Influenza in the United States—An Annualized Regression Approach Using Multiple-Cause Mortality Data], J. Dushoff ''et al.'', Am. J. Epidemiol. 163:181-7, 2006.</ref>. While it is difficult to estimate the lives saved by these drugs, the number seems likely to be large.
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===Sandboxes===
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*[[Sandbox1rpu]] working out configuration&isosurfaces&dots problems
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*[[Sandbox2hvy]] test for dots in another file
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* [[Sandbox CsrA]]
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* [[Sandbox TestMultiSurface]]
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===Protected Sandbox Pages===
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*[[User:Wayne Decatur/Protected Sandbox Pages|My Protected Sandbox Pages]]
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* [[HIV-1_protease|HIV protease structure]] was used in designing [http://en.wikipedia.org/wiki/Protease_inhibitor_(pharmacology) anti-retroviral protease inhibitors] that, as a component of [http://en.wikipedia.org/wiki/Antiretroviral_drug Highly Active Anti-Retroviral Therapy (HAART)], have added many high-quality years to the lives of HIV infected individuals. While HAART greatly extends life in HIV infected patients, it is not a cure, and these patients may eventually succumb to AIDS. ''References and quantitation needed.''
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===Protected Topic Pages===
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*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit]]
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*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]]
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*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome]]
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*[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
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*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
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*[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
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*[[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
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*[[User:Wayne Decatur/kink-turn motif]]
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*[[User:Wayne Decatur/Teaching Proteopedia]]
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*[[User:Wayne Decatur/Editing Getting Unremediated PDB Files]]
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*[[User:Wayne Decatur/Moving Components or Parts of Structures]]
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*[[User:Wayne Decatur/Generate Unfolded Structures]]
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*[[User:Wayne Decatur/Alter Disulfide Bonds in a Structure ]]
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*[[User:Wayne Decatur/4ay9 pymol]]
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*[[User:Wayne Decatur/Gal 4]]
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*[[User:Wayne Decatur/Homology Modeling]]
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*[[User:Wayne Decatur/Sequence analysis tools]]
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*[[User:Wayne Decatur/Structure analysis tools]]
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*[[User:Wayne Decatur/Molecular modeling tools]]
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*[[User:Wayne Decatur/BioWikis]]
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*[[User:Wayne Decatur/Code for Molecular Structure and Visualization Work]]
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*[[User:Wayne Decatur/I-Ppo Morph Methods]]
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*[[User:Wayne Decatur/3kg2 Morph Methods]]
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*[[User:Wayne Decatur/3fpn Morph methods]]
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*[[User:Wayne Decatur/3ewsSLASH3g0h Morph methods]]
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*[[User:Wayne Decatur/humanaGal3hg2toothers morph methods]]
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*[[User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods]]
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*[[User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods]]
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*[[User:Wayne Decatur/Converting Exported Proteopedia Pages from Jmol to JSmol]]
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==See Also==
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===Templates===
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*[[User:Wayne Decatur/Templates|My Templates]]
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*[http://www.umass.edu/microbio/rasmol/1st_xtls.htm Earliest Solutions for Macromolecular Crystal Structures]
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===Help===
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*[[Personal favorites]]
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*[[:Proteopedia:Problems]]
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*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring.
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*[http://wiki.jmol.org/index.php?title=Main_Page Jmol Wiki]
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==References==
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===Useful Resources===
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*[http://polyview.cchmc.org/polyview3d.html Polyview-3D]
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*[http://jena3d.fli-leibniz.de/ Jena3D Viewer]
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<references />
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===Wikitext help===
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*[http://en.wikipedia.org/wiki/Help:URL#URLs_in_external_links URLS in external links has the codes for using characters that aren't A-Z a-z 0-9 ._\/~%-+&#?!=()@ in links]
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<!--I needed that for my linking to my publications at PubMed in order to generate brackers for [au]-->
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*[http://howto.wikia.com/wiki/Guide_to_Wikitext_Markup_Language_(wiki_code) Guide to Wikitext Markup Language (wiki code)]
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*[http://en.wikipedia.org/wiki/How_to_edit How to edit] illustrates use of nowiki and pre tags.
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*[http://howto.wikia.com/wiki/Howto_use_wikitext_(quick_cheat_sheet) Wikitext quick cheat sheet] also has how to make link to categories, too
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*[http://meta.wikimedia.org/wiki/Help:Category Categories can be linked to with colon in front]
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*[http://meta.wikimedia.org/wiki/Help:HTML_in_wikitext HTML in wikitext]<!--apparently I should be using <span> tags and not <font> as <font> is deprecated now-->
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*[http://en.wikipedia.org/wiki/Template:Annotated_image/doc/Samples Allows cropping of images, in addition to annotating].
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*[http://en.wikipedia.org/wiki/Table_markup WikiTable Markup Guide]
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*[http://en.wikibooks.org/wiki/Editing_Wikitext/Tables Editing Wikitext/Tables]
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*[http://en.wikipedia.org/wiki/Wikipedia:Images_linking_to_articles Images: linking to articles using wikitext]

Current revision

Wayne Decatur in front row of Eilen Jewel private performance November 9th, 2008 at Williamsburg, MA Grange Hall

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 at Github

Wayne's publications listed at the the U.S. National Library of Medicine's PubMed database

email: Image:Decatur email.png


Some Proteopedia Pages to Which I've Contributed

Molecules: Topic Pages

Topic Pages - Structural Bioinformatics

Topic Pages - Education

Meta Pages

Workshops, Lectures, and Seminars

Personal Quicklinks

All Protected Pages

Files Uploaded

Sandboxes

Protected Sandbox Pages

Protected Topic Pages

Templates

Help

Useful Resources

Wikitext help

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Jaime Prilusky, Eran Hodis

Retrieved from "http://52.214.119.220/wiki/index.php/User:Wayne_Decatur"
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