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Ribbon diagram
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<h2 id="history">History</h2> <p>The first ribbon diagrams, hand-drawn by <a href="/facts/Jane_S._Richardson/maU1TjAh">Jane S. Richardson</a> in 1980 (influenced by earlier individual illustrations),<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> were the first schematics of 3D protein structure to be produced systematically.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a><a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> They were created to illustrate a classification of protein structures for an article in <i>Advances in Protein Chemistry</i><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> (now available in annotated form on-line at <a href="http://kinemage.biochem.duke.edu/teaching/anatax/">Anatax</a>). These drawings were outlined in pen on tracing paper over a printout of a <a href="/facts/Alpha_and_beta_carbon/E44SeQ1L">Cα</a> trace of the atomic coordinates, and shaded with colored pencil or pastels;<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> they preserved positions, smoothed the backbone path, and incorporated small local shifts to disambiguate the visual appearance.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> As well as the triose isomerase ribbon drawing at the right, other hand-drawn examples depicted <a href="https://commons.wikimedia.org/w/index.php?title=File:PrealbuminDimer_ribbon.jpg">prealbumin</a>, <a href="https://commons.wikimedia.org/w/index.php?title=File:Flavodoxin_ribbon_BWline.jpg">flavodoxin</a>, and <a href="https://commons.wikimedia.org/w/index.php?title=File:2SOD_ribbon_pastel.jpg">Cu,Zn superoxide dismutase</a>. </p><p>In 1982, <a href="/facts/Arthur_M._Lesk/BfrpJ2Ug">Arthur M. Lesk</a> and co-workers first enabled the automatic generation of ribbon diagrams through a computational implementation that uses <a href="/facts/Protein_Data_Bank/oUhq4ABD">Protein Data Bank</a> files as input.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> This conceptually simple <a href="/facts/Algorithm/fnl5NmRt">algorithm</a> fit <a href="/facts/Cubic_polynomial/t67bqD6c">cubic polynomial</a> <a href="/facts/B-spline/MLTCWCEd">B-spline</a> curves to the peptide planes. Most modern graphics systems provide either B-splines or <a href="/facts/Hermite_spline/L8UWpNT5">Hermite splines</a> as a basic drawing primitive. One type of spline implementation passes through each Cα guide point, producing an exact but choppy curve. Both hand-drawn and most computer ribbons (such as those shown here) are smoothed over about four successive guide points (usually the peptide midpoint) to produce a more visually pleasing and understandable representation. To give the right radius for helical spirals while preserving smooth β-strands, the splines can be modified by offsets proportional to local curvature, as first developed by Mike Carson for his Ribbons program<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> and later adopted by other molecular graphics software, such as the open-source Mage program for <a href="/facts/Kinemage/dt3bDBt4">kinemage</a> graphics<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> that produced the ribbon image at top right (other examples: <a href="https://commons.wikimedia.org/w/index.php?title=File:1xk8_trimer_ribbon.jpg">1XK8 trimer</a> and <a href="https://commons.wikimedia.org/w/index.php?title=File:DNApolymerase-DNA_complex_2HHV_ribbon.jpg">DNA polymerase</a>). </p><p>Since their inception, and continuing in the present, ribbon diagrams have been the single most common representation of protein structure and a common choice of cover image for a journal or textbook. </p> <h3>Current computer programs</h3> <p>One popular program used for drawing ribbon diagrams is Molscript. Molscript utilizes <a href="/facts/Hermite_spline/L8UWpNT5">Hermite splines</a> to create coordinates for coils, turns, strands, and helices. The curve passes through all its control points (<a href="/facts/C%CE%B1/E44SeQ1L">Cα</a> atoms) guided by direction vectors. The program was built based on traditional molecular graphics by <a href="/facts/Arthur_M._Lesk/BfrpJ2Ug">Arthur M. Lesk</a>, Karl Hardman, and John Priestle.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> <a href="/facts/Jmol/Ek2m784k">Jmol</a> is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: <a href="https://commons.wikimedia.org/w/index.php?title=File:Urease-1E9Z.jpg">urease</a>) and MolMol (example: <a href="https://commons.wikimedia.org/w/index.php?title=File:1lkkA_SH2_domain.png">SH2 domain</a>) also produce ribbon images. KiNG<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> is the Java-based successor to Mage (examples: <a href="https://commons.wikimedia.org/w/index.php?title=File:AlphaHemolysin_membrane_heptamer_7AHL_VwDownPore.jpg">α-hemolysin top view</a> and <a href="https://commons.wikimedia.org/w/index.php?title=File:AlphaHemolysin_membrane_heptamer_7AHL_sideVw.jpg">side view</a>). </p><p><a href="/facts/UCSF_Chimera/x4JpEHlH">UCSF Chimera</a> is a powerful molecular modeling program that also includes <a href="/facts/Scientific_visualization/p0yPc1X5">visualizations</a> such as ribbons, notable especially for the ability to combine them with contoured shapes from cryo-<a href="/facts/Electron_microscopy/XtaBktwF">electron microscopy</a> data.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> <a href="/facts/PyMOL/SbMJ9lPl">PyMOL</a>, by <a href="/facts/Warren_DeLano/7F8jut2X">Warren DeLano</a>,<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> is a popular and flexible molecular graphics program (based on <a href="/facts/Python_(programming_language)/YbuGqofa">Python</a>) that operates in interactive mode and also produces presentation-quality 2D images for ribbon diagrams and many other representations. </p> <h2 id="features">Features</h2> <table><tbody><tr><th>Secondary structure<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a><a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a></th><th></th></tr><tr><td>α-Helices</td><td>Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides.</td></tr><tr><td>β-Strands</td><td>Arrows with thickness, about one-quarter as thick as they are wide, showing direction and twist of the strand from amino to carboxy end. β-sheets are seen as unified because neighboring strands twist in unison.</td></tr><tr><th>Loops and miscellaneous</th><th></th></tr><tr><td>Nonrepetitive loops</td><td>Round ropes that are fatter in the foreground and thinner towards the back, following smoothed path of Cα trace.</td></tr><tr><td>Junctions between loops and helices</td><td>Round rope that gradually flattens out into a thin helical ribbon.</td></tr><tr><th>Other features</th><th></th></tr><tr><td>Polypeptide direction,<p>NH2 and COOH termini</p></td><td>Small arrows on one or both of the termini, or letters. For β-strands, the direction of the arrow is sufficient. Today, the direction of the polypeptide chain is often indicated by a colour ramp.</td></tr><tr><td>Disulfide bonds</td><td>Interlocked SS symbol or a zigzag, like a stylized lightning stroke.</td></tr><tr><td>Prosthetic groups or inhibitors</td><td>Stick figures, or <a href="/facts/Ball-and-stick_model/0FQhyys8">ball & stick</a>.</td></tr><tr><td>Metals</td><td>Spheres.</td></tr><tr><td>Shading and colour</td><td>Shading or colour adds dimensionality to the diagram. Generally, the features at the front are the highest in contrast and those towards the back are the lowest.</td></tr></tbody></table> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Molecular_graphics/rLuIm8hP">Molecular graphics</a></li></ul> Wikimedia Commons has media related to Ribbon diagrams. <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Smith, Thomas J. (October 27, 2005). "Displaying and Analyzing Atomic Structures on the Macintosh". Danforth Plant Science Center. Archived from the original on 28 March 2002. <a href="https://web.archive.org/web/20020328153147/http://www.danforthcenter.org/smith/molview/over/overview.html" target="_blank">https://web.archive.org/web/20020328153147/http://www.danforthcenter.org/smith/molview/over/overview.html</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Richardson, D. C.; Richardson, J. S. (January 2002). "Teaching Molecular 3-D Literacy". Biochemistry and Molecular Biology Education. 30 (1): 21–26. doi:10.1002/bmb.2002.494030010005. <a href="https://doi.org/10.1002%2Fbmb.2002.494030010005" target="_blank">https://doi.org/10.1002%2Fbmb.2002.494030010005</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Richardson, Jane S. (2000), "Early ribbon drawings of proteins", Nature Structural Biology, 7 (8): 624–625, doi:10.1038/77912, PMID 10932243, S2CID 52856546. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Richardson, Jane S. (2000), "Early ribbon drawings of proteins", Nature Structural Biology, 7 (8): 624–625, doi:10.1038/77912, PMID 10932243, S2CID 52856546. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Richardson, Jane S. (1985), "Schematic drawings of protein structures", Diffraction Methods for Biological Macromolecules Part B, Methods in Enzymology, vol. 115, pp. 359–380, doi:10.1016/0076-6879(85)15026-3, ISBN 978-0-12-182015-2, PMID 3853075. <a href="978-0-12-182015-2" target="_blank">978-0-12-182015-2</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Richardson, Jane S. (1981), "The Anatomy and Taxonomy of Protein Structure", Anatomy and Taxonomy of Protein Structures, Advances in Protein Chemistry, vol. 34, pp. 167–339, doi:10.1016/S0065-3233(08)60520-3, ISBN 978-0-12-034234-1, PMID 7020376. <a href="978-0-12-034234-1" target="_blank">978-0-12-034234-1</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>"Science's 'Mother of Ribbon Diagrams' celebrates 50 years at Duke". Duke Stories. 2018-10-19. Retrieved 2020-06-09. <a href="https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke" target="_blank">https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Richardson, Jane S. (1985), "Schematic drawings of protein structures", Diffraction Methods for Biological Macromolecules Part B, Methods in Enzymology, vol. 115, pp. 359–380, doi:10.1016/0076-6879(85)15026-3, ISBN 978-0-12-182015-2, PMID 3853075. <a href="978-0-12-182015-2" target="_blank">978-0-12-182015-2</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Lesk, Arthur M.; Hardman, Karl D. (1982), "Computer-Generated Schematic Diagrams of Protein Structures", Science, 216 (4545): 539–540, Bibcode:1982Sci...216..539L, doi:10.1126/science.7071602, PMID 7071602. <a href="/wiki/Science_(journal)" target="_blank">/wiki/Science_(journal)</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Carson, M.; Bugg, C. E. (1986), "Algorithm for Ribbon Models of Proteins", Journal of Molecular Graphics, 4 (2): 121–122, doi:10.1016/0263-7855(86)80010-8. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Richardson, D. C.; Richardson, J. S. (January 1992), "The kinemage: a tool for scientific communication", Protein Science, 1 (1): 3–9, doi:10.1002/pro.5560010102, PMC 2142077, PMID 1304880 <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>MolScript v2.1: About the program <a href="http://www.avatar.se/molscript/doc/about.html" target="_blank">http://www.avatar.se/molscript/doc/about.html</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Chen, V. B.; Davis, I. W.; Richardson, D. C. (2009), "KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program", Protein Science, 18 (11): 2403–2409, doi:10.1002/pro.250, PMC 2788294, PMID 19768809 <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Goddard, Thomas D.; Huang, Conrad C.; Ferrin, Thomas E. (2005), "Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies", Structure, 13 (3): 473–482, doi:10.1016/j.str.2005.01.006, PMID 15766548. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Brunger, Axel T.; Wells, James A. (2009), "Warren L. DeLano, 21 June 1972-3 November 2009", Nature Structural & Molecular Biology, 16 (12): 1202–1203, doi:10.1038/nsmb1209-1202, PMID 19956203. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Richardson, Jane S. (1985), "Schematic drawings of protein structures", Diffraction Methods for Biological Macromolecules Part B, Methods in Enzymology, vol. 115, pp. 359–380, doi:10.1016/0076-6879(85)15026-3, ISBN 978-0-12-182015-2, PMID 3853075. <a href="978-0-12-182015-2" target="_blank">978-0-12-182015-2</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Richardson, Jane S. (1981), "The Anatomy and Taxonomy of Protein Structure", Anatomy and Taxonomy of Protein Structures, Advances in Protein Chemistry, vol. 34, pp. 167–339, doi:10.1016/S0065-3233(08)60520-3, ISBN 978-0-12-034234-1, PMID 7020376. <a href="978-0-12-034234-1" target="_blank">978-0-12-034234-1</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> </ol>