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<div style="font-size:175%; padding-top:0.5em; padding-left:30.0px;">Welcome to Proteopedia,</div>
<div style="font-size:175%; padding-top:0.5em; padding-left:30.0px;">Welcome to Proteopedia,</div>
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<div style="border:0px; padding:0px; margin=0px; line-height:2.0em; padding-left:30.0px;">The free, collaborative 3D encyclopedia</div>
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<div style="border:0px; padding:0px; margin=0px; line-height:2.0em; padding-left:30.0px;">The free, collaborative 3D encyclopedia of proteins & other molecules</div>
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<div style="border:0px; padding:0px; margin=0px; line-height:0em; padding-bottom:0.8em; padding-left:30.0px;">of proteins & other molecules</div>
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[[About]] [[Editing]] [[Help]] [[Contents]] [[Topic Pages]] [[What's New]]
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<td align="left" width="50%">[[Proteopedia:About|About]] <font color="blue">•</font> [[Help:Editing|Editing]] <font color="blue">•</font> [[Help:Contents|Help]]</td>
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<td align="right" width="50%">[[Proteopedia:Video_Guide|Video Guide]] <font color="blue">•</font> [[Proteopedia:Interesting_Pages|Content (Topic Pages)]] <font color="blue">•</font> [[Proteopedia:What%27s_New|What's New]]</td>
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<th style="background: #94FFC8;" width ="100%" colspan="2">
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|<div style="font-size:120%">Currently featured article</div>
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<div style="font-size:120%" align="left">Currently featured article</div>
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|<applet load='1eve' size='300' frame='true' align='right' caption='Insert caption here' scene='Main_Page/E2020_in_ache_spinning/1'/>
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|The anti-Alzheimer's drug E2020 (marketed as Aricept&reg;) is an inhibitor that binds acetylcholinesterase (AChE) with high affinity. The X-ray structure of the E2020-AChE (AChE from ''Torpedo california'') complex shows that E2020 has a '''<scene name='1eve/E2020_close_up_with_84_279/12'>unique orientation</scene>''' along the active-site gorge, extending from the anionic subsite ('''<scene name='1eve/E2020_close_up_with_84lbld/6'>W84</scene>''') of the active site, at the bottom, to the peripheral anionic site ('''<scene name='1eve/E2020_close_up_with_84_279lbld/4'>near W279</scene>'''), at the top, via aromatic stacking interactions with conserved aromatic acid residues. E2020 does not, however, interact directly with either the catalytic triad or the 'oxyanion hole' but only '''<scene name='1eve/E20_interactionshown/7'>indirectly via solvent molecules</scene>'''.
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<applet load='2q66' size='300' frame='false' scene='Proteopedia:Main_page_develop/2q66_initial/3' />
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===<span style="color:green">Green</span> links change the 3D image!===
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<div style="font-size:130%; line-height:2.0em"><span style="color:green" align="center">Green</span> links change the 3D image!</div>
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<div style="font-size:200%; line-height:2.0em">[[2q66]] - Poly(A) polymerase</div>
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Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. … In the <scene name='2q66/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for ATP. The magnesium is coordinated by <scene name='2q66/2q66_asp/2'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='2q66/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. [[2q66|Read more...]]
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<table style="background: #D1FFE7; border:1px solid #94FFC8" cellspacing="5px" cellpadding="10px" width="100%">
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<div style="font-size:120%" align="left">Browse</div>
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<div style="font-size:120%; line-height:2.0em">Favorites</div>
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<div style="font-size:120%; line-height:2.0em">Find my protein/molecule</div>
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<div style="font-size:120%; line-height:2.0em">What's new?</div>
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<td width="33%" valign="top">
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* [[Hemoglobin]] - the protein in your blood responsible for oxygen transport
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* [[HIV-1 protease]] - a protein made by the HIV virus that is crucial to its infectious capacity
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* [[Lac repressor]] - a protein that controls the expression of bacterial enzymes involved in lactose metabolism
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<div align="right">[[Favorites|More]]...</div>
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<td width="34%" valign="top">
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* All [[PDB]] entries (over 54,000) have pages
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<inputbox>
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type=search
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width=20
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buttonlabel=Go
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searchbuttonlabel=Search
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* ''Go'' takes you directly to the page if it exists,
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* ''Search'' gives you search results
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<div align="right">[[Help:Searching|More]]...</div>
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<td width="33%" valign="top">
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* [[2q66]] - yeast poly(a)-polymerase, adds poly-A tails to nascent messenger RNAs
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* [[Hydrogen bonds]]
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* [[Morphs]] - visualizing conformational changes
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<div align="right">[[Proteopedia:What%27s_New| More]]...</div>
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===See more!===
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<table style="background: #D1FFE7; border:1px solid #94FFC8" cellspacing="5px" cellpadding="10px" width="100%">
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<big>The [[Proteopedia:Video_Guide | Proteopedia Video Guide]] is a narrated video guide that serves both as a starting point as well as a reference. </big>
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<div style="font-size:120%" align="left">Want to contribute?</div>
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<div align="center">Pages are easy to create and edit, and <font color='green'>'''Green links'''</font> are easy to make! </div>
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<div style="font-size:120%; line-height:2.0em">Step 1</div>
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<td>
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<div style="font-size:120%; line-height:2.0em">Step 2</div>
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<div style="font-size:120%; line-height:2.0em">Step 3</div>
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[[Special:RequestAccount|Request an account]].<br/>''(Members of the scientific community, including students and educators.)''
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Get started with our narrated [[Proteopedia:Video_Guide|video guide]], then use our [[Help:Editing|editing-help page]] as a reference.
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Help us expand an existing page like [[1twc]] or [[Prion proteins]],
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[[Image:Ipodtouch_hero_20080205.png|left|100px]]
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Or [[Help:Editing#How_To_Create_A_New_Page|start a new page]] on your favorite molecule or topic.
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===[[Proteopedia:Page of the Year Competition|Page of the Year Competition]]===
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We're giving away a top-of-the-line [http://www.apple.com/ipodtouch/ 32Gb iPod touch] (generously donated by [http://www.idigital.co.il iDigital], [http://www.apple.com Apple's] representatives in Israel) to the winner of Proteopedia's Page of the Year Competition! To learn more and to enter, visit [[Proteopedia:Page of the Year Competition]].
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{{Clear}}
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====Favorites====
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We could use pages on [[DNA]], [[Trypsin]], and [[Myoglobin]], among [[Wanted pages|others]].
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Here are several of our favorite pages. Visit them to get a feeling for Proteopedia:
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* [[Hemoglobin]]
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</table>
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* [[HIV-1 protease]]
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* [[1eve | Acetylcholinesterase with the anti-Alzheimer's drug Aricept bound]]
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* [[Photosystem II]]
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* [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
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&nbsp; &nbsp;
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* [[Lac repressor]] with a [[Morphs|morph]] of it bending the DNA operator.
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* [[1v04 | Serum Paraoxonase-1 created by directed evolution]].
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* [[Recoverin, a calcium-activated myristoyl switch]] with [[Morphs|morphs]] of a dramatic conformational change.
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* [[1ogs | Human acid-beta-glucosidase]]
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* See also: [[Personal_favorites | Personal favorites pages]]
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====Browse!====
 
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<table border="0"><tr><td>
 
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* [[Proteopedia:What's New|What's New in Proteopedia?]]
 
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* [[Proteopedia:Interesting_Pages | Topic pages]]
 
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* [[Highest_impact_structures | Highest impact structures of all time]]
 
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* [[About Macromolecular Structure]]
 
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&nbsp; &nbsp;
 
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* [[Personal_favorites | Personal favorites]]
 
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* [[Proteopedia:News|News]]
 
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* [[Special:Statistics | Statistics]]
 
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* [[Believe_It_or_Not%21 | Believe It or Not!]]
 
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<table style="background: #D1FFE7; border:1px solid #94FFC8" cellspacing="5px" cellpadding="10px" width="100%">
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<tr>
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<th style="background: #94FFC8;" width ="100%" colspan="3">
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<div style="font-size:120%" align="left">What can Proteopedia do for me?</div>
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</tr>
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<tr>
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<td>
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<div style="font-size:120%; line-height:2.0em">Scientists and Students</div>
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<div style="font-size:120%; line-height:2.0em">Educators</div>
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<td>
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<div style="font-size:120%; line-height:2.0em">Structural researchers</div>
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</td>
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</tr>
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<tr>
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<td width="33%" valign="top">
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* Understand and communicate protein 3D structure-function relationships
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** Example: [[1wsu|Elongation factor SelB]], the protein responsible for adding the 21<sup>st</sup> amino acid selenocysteine to a growing protein chain in bacteria, featured in the [[Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages#Molecule_of_the_Month_.28MotM.29_Series|Molecule of the Month]] at the PDB.
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</td>
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<td width="34%" valign="top">
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* Develop [[Teaching Scenes, Tutorials, and Educators' Pages|tutorials or molecular scenes]] to project during lectures
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* [[Teaching Strategies Using Proteopedia|Assign students to construct pages]] in Proteopedia for [[Student Projects|class projects]] or reports
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''(You may [[Help:Protected Pages|protect your teaching pages from editing]] by others.)''
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* Create [[3btp|supplementary material]] for your journal publications
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* Create pages about your [[Research Groups|research team or institute]], highlighting structures you have researched.
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''(You may [[Help:Protected Pages|protect such pages from editing]] by others, or [[Proteopedia:Workbench|unwanted viewing]] pre-publication.)''
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===How can I find my protein/molecule?===
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<big>'''Search'''</big> Proteopedia using the search box in the toolbar to the left. See also [[Help:Searching]].
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<table style="background: #D1FFE7; border:1px solid #94FFC8" cellspacing="5px" cellpadding="10px" width="100%">
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Proteopedia already contains '''>50,000 pages''', including an automatically-generated page for every published macromolecular 3D structure (to see some of these, click ''Random Page'' in the navigation box at the upper left), plus [[Proteopedia:Topic Pages | Topic Pages]] providing an overview of a class of molecules or other structural topics.
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===Want to contribute?===
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<div style="font-size:120%" align="left">Read the paper</div>
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<font color='green'>Green links</font> are easy to make! We encourage you to '''edit pages freely''' and to '''[[Help:Editing#How_To_Create_A_New_Page | add new pages]].
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You will need a user account in order to edit or add pages. Please go ahead and '''[[Special:RequestAccount|request a user account]]'''.
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<td valign="top">
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''Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules'', '''Genome Biology''' 2008, 9:R121 [http://genomebiology.com/2008/9/8/R121 doi:10.1186/gb-2008-9-8-r121]
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If you have any questions, you can email {{Template:Contact}}.
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These resources may help you familiarize yourself with the editing process. Trust us, the editing process is very simple: All text is edited the same way that Wikipedia is edited, so it must be easy! And all scenes (green links) are created using our user-friendly ''Scene authoring tools''. Of course it helps to familiarize yourself with the site and how to go about editing, so check out these resources:
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*<big>The [[Proteopedia:Video_Guide | Proteopedia Video Guide]] is a narrated video guide that serves both as a starting point as well as a reference. </big>
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*The [[Help:Editing | '''Editing Help Page''']].
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*The help page for the [[Scene authoring tools]].
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* [[Proteopedia:Policies]] and the [[Proteopedia: Email list]]
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===What Can Proteopedia Do For Me?===
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* Scientists and Students: a reference resource for understanding protein 3D structure-function relationships. Example: [[1eve | Acetylcholinesterase bound to Aricept, an anti-Alzheimer's drug]].
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* Educators: develop tutorials or molecular scenes to project during lectures, or for student use. Examples: [[Teaching Scenes, Tutorials, and Educators' Pages]]. Assign students to construct pages in Proteopedia for class projects or reports: see [[Student Projects]]. See also [[Teaching Strategies Using Proteopedia]].
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You may protect your teaching pages from unwanted editing by others -- see [[Help:Protected Pages]].
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* Structural Researchers: create supplementary materials for your journal publications, and pages about your research team or institute, highlighting structures you have researched. For examples, see [[Research Groups]].
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You may protect such pages from unwanted editing by others -- see [[Help:Protected Pages]].
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===Proteopedia Mission Statement===
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To collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists.
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===Goals for Proteopedia===
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* To serve as a forum for the scientific community to share, retrieve and discuss information related to proteins, macromolecules, and small molecules and chemicals of interest.
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* To continue to develop the concept of tying text to three-dimensional, interactive images.
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* To maintain low barriers for contribution.
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* To foster collaborations between students and experts, signed with their real names.
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===About Proteopedia: How to Cite Proteopedia (''Genome Biology'' Publication) / News / Contact ===
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On the page '''[[Proteopedia:About | About Proteopedia]]''' you will find information about how to cite Proteopedia, and its contents, implementation, policies and credits. At '''[[Proteopedia: News]]''' you will find current events concerning Proteopedia, such as press reports, blogs, meeting reports and seminars, training workshops, and a list of databases and structural bioinformatics resources that offer links to Proteopedia.
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If you have any questions, please contact {{Template:Contact}}.
 
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===Mugs and T-Shirts===
 
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Proudly show your love for Proteopedia and help spread Proteopedia's wonders with highly coveted mugs and T-shirts from [http://www.cafepress.com/molviz4 cafepress.com], featuring the original Proteopedia logo by Tali Wiesel. Cafepress is a website that prints custom images on mugs and T-shirts, and is unaffiliated with Proteopedia. Proteopedia collects no money from your purchase.
 
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__NOEDITSECTION____NOTOC___
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Current revision

Welcome to Proteopedia,
The free, collaborative 3D encyclopedia of proteins & other molecules
About • Editing • Help Video Guide • Content (Topic Pages) • What's New
Currently featured article

PDB ID 2q66

Drag the structure with the mouse to rotate
Green links change the 3D image!
2q66 - Poly(A) polymerase

Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. … In the , the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for ATP. The magnesium is coordinated by , and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the . Read more...

Browse
Favorites
Find my protein/molecule
What's new?
  • Hemoglobin - the protein in your blood responsible for oxygen transport
  • HIV-1 protease - a protein made by the HIV virus that is crucial to its infectious capacity
  • Lac repressor - a protein that controls the expression of bacterial enzymes involved in lactose metabolism
More...
  • All PDB entries (over 54,000) have pages
  • Go takes you directly to the page if it exists,
  • Search gives you search results
More...
  • 2q66 - yeast poly(a)-polymerase, adds poly-A tails to nascent messenger RNAs
  • Hydrogen bonds
  • Morphs - visualizing conformational changes
Want to contribute?
Pages are easy to create and edit, and Green links are easy to make!
Step 1
Step 2
Step 3

Request an account.
(Members of the scientific community, including students and educators.)

Get started with our narrated video guide, then use our editing-help page as a reference.

Help us expand an existing page like 1twc or Prion proteins,

Or start a new page on your favorite molecule or topic.

We could use pages on DNA, Trypsin, and Myoglobin, among others.

What can Proteopedia do for me?
Scientists and Students
Educators
Structural researchers
  • Understand and communicate protein 3D structure-function relationships

(You may protect your teaching pages from editing by others.)

(You may protect such pages from editing by others, or unwanted viewing pre-publication.)

Read the paper

Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Genome Biology 2008, 9:R121 doi:10.1186/gb-2008-9-8-r121


_

Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis

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