Interactive 3D Complements in Proteopedia: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, David Canner, Eric Martz, Joel L. Sussman

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 Articles in Proteopedia can be designed to complement publications in scientific journals. A link, within the publication, to an ''interactive 3D complement'' (I3DC) in Proteopedia can enable readers to rotate molecular scenes having the same initial orientation, color schemes, and labeling as figures in the publication. Links to the interactive 3D complement in Proteopedia can be placed in the text of the publication, and/or in the .doc file included on the journal website as [[#I3DC vs. Supplementary Materials|supplementary materials]]. The I3DC article can be developed in advance of publication, yet hidden from viewing by visitors to Proteopedia until publication occurs (see [[Proteopedia:Workbench]]). Authors of the associated publications are able and encouraged to review the I3DC page before publication, and to interact with the [[Proteopedia:Team#Proteopedia_I3DC_Board|Proteopedia editor]] at any time. I3DC are [[#Protection From Editing|protected]] from editing by anyone.
-Proteopedia is working with Journals to develop, in close collaboration with authors, interactive 3D complement articles in Proteopedia, thus rendering the structural data more comprehensible to a wider audience. In addition, Proteopedia welcomes author-initiated development of interactive 3D complement articles for individual publications in any journal.
+Proteopedia is working with Journals to develop, in close collaboration with authors, interactive 3D complement articles in Proteopedia, thus rendering the structural data more comprehensible to a wider audience. In addition, Proteopedia welcomes author-initiated development of interactive 3D complement articles for individual publications in any journal. '''List of [[Proteopedia:I3DC|I3DC pages]]''' available for open access.
-For more details, please contact <email>manuscript@proteopedia.org</email>
+For more details, please [[Special:Contact|Contact]] us.
 ==Journals Adopting I3DC==
-[[Image:JBIC.jpg|left|120px|]]
+[[Image:Jbic_logo.jpg|left|120px|]]
 The [[Journal_of_Biological_Inorganic_Chemistry|Journal of Biological Inorganic Chemistry]] seeks to promote this field internationally. This journal is primarily concerned with advances in the understanding of systems involving one or more metal ions set in a biological matrix--particularly, metalloproteins and metal-nucleic acid complexes--in order to understand biological function at the atomic level. Manuscripts describing high quality and original research concerned with metal ions or other inorganic species and having biological relevance are invited for submission to this journal. Mini-reviews, Reports, and Commentaries are also encouraged. Examples can be found in the [[Journal_of_Biological_Inorganic_Chemistry|list of I3DC articles for JBIC]].
 {{Clear}}
 ==Author-Initiated I3DC==
-Proteopedia encourages authors of any scientific publication to develop an interactive 3D complement in Proteopedia. Members of the Proteopedia team stand ready to assist: {{Template:Contact}}. Here are some examples of author-initiated I3DC:
+Proteopedia encourages authors of any scientific publication to develop an interactive 3D complement in Proteopedia. Members of the Proteopedia team stand ready to assist: [[Special:Contact|Contact]]. Here are some examples of author-initiated I3DC. Years are dates of journal publication.
-* The publication of [[3btp]] in ''Proc. Natl. Acad. Sci. USA''<ref>PMID:18678909</ref> was accompanied by an I3DC.
+===2015-Present===
-*[[User:Oleg_Kovalevskiy/Engineered mutants of HlyIIR|Engineered mutants of HlyIIR]] provides supplementary figures for a [http://www3.interscience.wiley.com/journal/123272500/abstract publication in ''Proteins'']<ref>PMID: 20225260</ref>.
+* 2021: Structure of Geobacter pili reveals secretory rather than nanowire behavior. Gu, Srikanth, ''et al., Nature'', in press. See [[Malvankar/3]].
+** See also [[Malvankar]], a list of I3DC for publications by this author.
+* 2019: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Wang, Gu ''et al., Cell'' <ref>PMID:30951668</ref>, see [[Malvankar/2]].
+* 2017: An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. Barker ''et al.'', ''BMC Biology'' <ref>PMID:29078764</ref>, see [[Samatey/5]].
+** See also [[Samatey]], a list of I3DC for publications by this author.
+* 2016: Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Matsunami ''et al.'', ''Nature Communications''<ref>PMID:27811912</ref>, see [[Samatey/4]].
+* 2016: Structural insights into bacterial flagellar hook similarities and specifities. Yoon ''et al.'', ''Scientific Reports''<ref>PMID: 27759043</ref>, see [[Samatey/3]].
+* 2016: Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in ''Salmonella enterica''. Matsunami ''et al.'', ''Scientific Reports''<ref>PMID: 27273476</ref>, see [[Samatey/2]].
+* 2016: Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of ''Geobacter sulfurreducens'' Pili. Xiao ''et al.''<ref>PMID: 27001169</ref>, ''Scientific Reports'', see [[Ke Xiao/1]].
+* 2015: Structural basis for metallic-like conductivity in microbial nanowires. Malvankar ''et al.''<ref>PMID: 25736881</ref>, see [[Journal:mBio:1]].
+===2008-2014===
+* 2013: Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins. V. A. Meshcheryakov, A. Kitao, H. Matsunami and F. A. Samatey. ''Acta Crystallographica D'' D69, 812-820. See [[Samatey/1]].
+* 2011: The publication of "Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex" in ''JSB''<ref>PMID: 21933716 </ref> was accompanied by an I3DC at [[Journal:JSB:1]].
+*2011: [[User:Janice C. Telfer/Group B SRCR domains]] provides interactive 3D complements linked into the discussion of the publication ''Scavenger receptor WC1 contributes to the γδ T cell response to Leptospira''<ref>PMID: 21227509</ref>.
+* 2011: The publication of "Structural linkage between ligand discrimination and receptor activation by type I interferon" in ''Cell''<ref>PMID: 21854986</ref> was accompanied by an I3DC at [[Journal:Cell:1]]. The structures in the paper were  of interferon and interferon receptor complexes:  [[3s98]] (IFNAR1ΔSD4), [[3s8w]] (IFNAR2-D2), [[3s9d]] (binary IFNα-IFNAR2 complex), [[3se4]] (ternary IFNω complex), and [[3se3]] (ternary IFNα complex).
+* 2011: The publication of "Antiviral Activity of 3(2H)- and 6-Chloro-3(2H)-Isoflavenes against Highly Diverged, Neurovirulent Vaccine-Derived, Type2 Poliovirus Sewage Isolates" in ''PLoS ONE''<ref>DOI 10.1371/journal.pone.0018360</ref> was accompanied by an I3DC at [[Journal:PLoS_ONE:1]].
+*2010: Interconversion of the Specificities of Human Lysosomal Enzymes Associated with Fabry and Schindler Diseases<ref>PMID: 20444686</ref> by Tomasic IB1, Metcalf MC, Guce AI, Clark NE, Garman SC. (J. Biol. Chem.) is illustrated at [[Garman lab: Interconversion of lysosomal enzyme specificities]].
+*2010: [[User:Oleg_Kovalevskiy/Engineered mutants of HlyIIR|Engineered mutants of HlyIIR]] provides interactive 3D complements for a [http://www3.interscience.wiley.com/journal/123272500/abstract publication in ''Proteins'']<ref>PMID: 20225260</ref>.
+* 2008: The publication of [[3btp]] in ''Proc. Natl. Acad. Sci. USA''<ref>PMID:18678909</ref> was accompanied by an I3DC.
 ==I3DC vs. Supplementary Materials==