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Inside a ribbon diagram - with VR
Inside a ribbon diagram - with VR
Published: 2016/02/18
Channel: Phil Trease
3D visualization of molecular surface and ribbon diagram with Virtual Reality
3D visualization of molecular surface and ribbon diagram with Virtual Reality
Published: 2017/04/10
Channel: Hanako Apple
six staged ribbon diagram for data representation powerpoint template
six staged ribbon diagram for data representation powerpoint template
Published: 2015/06/22
Channel: Steve Brumett
four staged triangle ribbon diagram with icons
four staged triangle ribbon diagram with icons
Published: 2015/09/16
Channel: Steve Brumett
four staged ribbon diagram with icons flat powerpoint design
four staged ribbon diagram with icons flat powerpoint design
Published: 2015/10/14
Channel: Steve Brumett
What Your Poop Says About You (For Serious)
What Your Poop Says About You (For Serious)
Published: 2016/08/20
Channel: Mama Natural
Project 2016 for Beginners Part 3: How to Use the Ribbon and Toolbars in MS Project 2016
Project 2016 for Beginners Part 3: How to Use the Ribbon and Toolbars in MS Project 2016
Published: 2016/05/26
Channel: Simon Sez IT
eight staged ribbon and icon diagram flat powerpoint design
eight staged ribbon and icon diagram flat powerpoint design
Published: 2015/10/20
Channel: PowerPoint
Understanding the Ribbon Interface
Understanding the Ribbon Interface
Published: 2014/08/04
Channel: CADLearning
Wire Edged Ribbon Bow
Wire Edged Ribbon Bow
Published: 2013/12/12
Channel: ThriftyFun
Learn to make the Ribbon Dance Quilt with Jenny!
Learn to make the Ribbon Dance Quilt with Jenny!
Published: 2017/02/24
Channel: Missouri Star Quilt Company
Origami - Paper Bow/Ribbon Tutorial Version 2 🎀 DIY 🎀
Origami - Paper Bow/Ribbon Tutorial Version 2 🎀 DIY 🎀
Published: 2013/11/10
Channel: Paper Kawaii - Origami Tutorials
Raspberry Pi 7
Raspberry Pi 7'' LCD Installation
Published: 2014/04/01
Channel: Smart Sain
How to cut, connect & power LED Strip Lighting
How to cut, connect & power LED Strip Lighting
Published: 2014/05/15
Channel: LED supplies
Visio 2013 for Beginners - Part 4 - How to Navigate the Ribbon in Visio 2013
Visio 2013 for Beginners - Part 4 - How to Navigate the Ribbon in Visio 2013
Published: 2015/05/07
Channel: Simon Sez IT
Ribbon Loading in the DTC 4500 | New York ID Badges | New York ID Cards
Ribbon Loading in the DTC 4500 | New York ID Badges | New York ID Cards
Published: 2013/02/19
Channel: ID Edge
Irritable Bowel Syndrome | IBS | Nucleus Health
Irritable Bowel Syndrome | IBS | Nucleus Health
Published: 2012/08/03
Channel: Nucleus Medical Media
Origami Layered Bow Tutorial 🎀 DIY Ribbon 🎀 Paper Kawaii
Origami Layered Bow Tutorial 🎀 DIY Ribbon 🎀 Paper Kawaii
Published: 2016/11/05
Channel: Paper Kawaii - Origami Tutorials
Create Influence Diagram in PowerPoint: Consulting Models Series #1
Create Influence Diagram in PowerPoint: Consulting Models Series #1
Published: 2013/08/29
Channel: Presentation Process
Ian Knot detailed tutorial - Professor Shoelace
Ian Knot detailed tutorial - Professor Shoelace
Published: 2014/08/02
Channel: ProfessorShoelace
MIDI Ribbon/Continuum Controller Kit
MIDI Ribbon/Continuum Controller Kit
Published: 2012/01/03
Channel: ZvonekContinuum
How to make a Solar Panel - Wiring, Soldering, and Cell Layout - Explained Simply!
How to make a Solar Panel - Wiring, Soldering, and Cell Layout - Explained Simply!
Published: 2013/10/05
Channel: desertsun02
Positive and Negative Charge
Positive and Negative Charge
Published: 2014/05/17
Channel: Bozeman Science
TaskMap Ribbon
TaskMap Ribbon
Published: 2011/04/01
Channel: taskmap
Paper/Ribbon Heart Origami Tutorial
Paper/Ribbon Heart Origami Tutorial
Published: 2015/07/01
Channel: BoBoWrapz
Time-lapse Shows How Anticancer and Antiviral Drugs Get Into Cells
Time-lapse Shows How Anticancer and Antiviral Drugs Get Into Cells
Published: 2017/04/17
Channel: Duke University
Diagram 389 WOW! Electron Pencil Ribbon Lasers Piezoelectric Crystals
Diagram 389 WOW! Electron Pencil Ribbon Lasers Piezoelectric Crystals
Published: 2017/02/06
Channel: theideagirlsays
Diagram 376 WOW! Electron Ribbon Lasers Positive Plasma
Diagram 376 WOW! Electron Ribbon Lasers Positive Plasma
Published: 2017/01/24
Channel: theideagirlsays
Zebra Label Printer Ribbon and Label Installation
Zebra Label Printer Ribbon and Label Installation
Published: 2015/12/12
Channel: MINDWARE ibc
Training: Make the switch to Visio 2013: The ribbon - Video 2 of 4
Training: Make the switch to Visio 2013: The ribbon - Video 2 of 4
Published: 2013/06/11
Channel: Office Videos
Origami - How to fold a paper Bow/Ribbon
Origami - How to fold a paper Bow/Ribbon
Published: 2013/11/10
Channel: Paper Kawaii - Origami Tutorials
Diagram 59 WOW! Higgs electron ribbon pulse beams
Diagram 59 WOW! Higgs electron ribbon pulse beams
Published: 2015/12/08
Channel: theideagirlsays
iPhone 6 Front Assembly Small Component Installation
iPhone 6 Front Assembly Small Component Installation
Published: 2015/06/03
Channel: ETrade Supply
Diagram 158 wow! Electron Ribbon Beams crystal Lattice UFO Engine
Diagram 158 wow! Electron Ribbon Beams crystal Lattice UFO Engine
Published: 2016/02/29
Channel: theideagirlsays
2-minute video tutorial: Ribbon quilt - quick and easy block
2-minute video tutorial: Ribbon quilt - quick and easy block
Published: 2017/07/15
Channel: Teresa DownUnder
How to: DJI Phantom 3 (and Phantom 2) Flex Ribbon Cable Replacement
How to: DJI Phantom 3 (and Phantom 2) Flex Ribbon Cable Replacement
Published: 2015/11/06
Channel: Drones Made Easy
3d Protein in Hololens
3d Protein in Hololens
Published: 2016/08/03
Channel: Mark Hoffman
Protein Rotation
Protein Rotation
Published: 2017/02/18
Channel: Jeramia Ory
How to Crochet A Shawl:  🎗️ Pink Ribbon Shawl
How to Crochet A Shawl: 🎗️ Pink Ribbon Shawl
Published: 2017/07/17
Channel: How to Crochet - The Crochet Crowd
9 Useful commands not in ribbon you should know   Microsoft word Tutorial
9 Useful commands not in ribbon you should know Microsoft word Tutorial
Published: 2017/07/07
Channel: HBN Infotech - Tutorials
Origami Tutorial: Hydrangea Ribbon Box (Dáša Ševerová and Shuzo Fujimoto)
Origami Tutorial: Hydrangea Ribbon Box (Dáša Ševerová and Shuzo Fujimoto)
Published: 2015/03/07
Channel: happyfolding.com - enjoy origami online
FARO Zone 3D Home Ribbon
FARO Zone 3D Home Ribbon
Published: 2017/07/05
Channel: FARO Global Customer Service
How to make big bows with wire edged ribbon.
How to make big bows with wire edged ribbon.
Published: 2014/11/23
Channel: Jani Lewis
Human insulin receptor tyrosine kinase in active conformation with IRS1 pYMXM site in its mouth
Human insulin receptor tyrosine kinase in active conformation with IRS1 pYMXM site in its mouth
Published: 2011/06/03
Channel: Anton-Scott Goustin
Excel 2013 for Beginners Part 8: The Excel Ribbon, Tabs, and Commands
Excel 2013 for Beginners Part 8: The Excel Ribbon, Tabs, and Commands
Published: 2014/06/11
Channel: Simon Sez IT
Microsoft Project Garis kolom dengan gridlines, timescale dan ribbon gantt chart wizard
Microsoft Project Garis kolom dengan gridlines, timescale dan ribbon gantt chart wizard
Published: 2017/05/23
Channel: Haloho Project
Draw a DNA Double Helix in Powerpoint
Draw a DNA Double Helix in Powerpoint
Published: 2015/10/08
Channel: Dinesh F
Ghosh Alzheimer
Ghosh Alzheimer's
Published: 2012/10/01
Channel: Purdue University
Origami Lucky Star Tutorial ⭐️ Easy DIY ⭐️ Paper Kawaii
Origami Lucky Star Tutorial ⭐️ Easy DIY ⭐️ Paper Kawaii
Published: 2016/10/26
Channel: Paper Kawaii - Origami Tutorials
Pc ribbon cable exciter and other experiments
Pc ribbon cable exciter and other experiments
Published: 2010/10/30
Channel: jonnydavro
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WIKIPEDIA ARTICLE

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Ribbon diagram of myoglobin bound to haem (sticks) and oxygen (red spheres) (PDB: 1MBO​)

Ribbon diagrams, also known as Richardson Diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the image at the right. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and lines or thin tubes for non-repetitive coils or loops. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.[1]

Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed the overall organization of the protein structure, reflecting its 3-dimensional information, and allowing for better understanding of a complex object both by the expert structural biologists and also by other scientists, students,[2] and the general public.

Ribbon schematic of triose P isomerase monomer (hand-drawn by J. Richardson, 1981) (PDB: 1TIM​)

History[edit]

Originally conceived by Jane S. Richardson in 1980 (influenced by earlier individual illustrations),[3] her hand-drawn ribbon diagrams were the first schematics of 3D protein structure to be produced systematically,[3][4] to illustrate a classification of protein structures for an article in Advances in Protein Chemistry[5] (now available in annotated form on-line at Anatax). These drawings were made in pen on tracing paper over a printout of a trace of the atomic coordinates; they preserved positions, smoothed the backbone path, and incorporated small local shifts to disambiguate the visual appearance.[4] As well as the TIM ribbon drawing at the right, other hand-drawn examples are for prealbumin, flavodoxin, and Cu,Zn superoxide dismutase.

In 1982, Arthur M. Lesk and co-workers first enabled automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input.[6] This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes. Most modern graphics systems provide either B-splines or Hermite splines 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 4 successive guide points (usually the peptide midpoint), to produce a more visually pleasing and understandable representation. In order 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[7] (figure at right) and later adapted by other molecular graphics software, such as the open-source Mage program for kinemage graphics[8] that produced the ribbon image at top right (other examples: 1xk8 trimer and DNA polymerase).

Since their inception, and continuing in the present, a ribbon diagram is the single most common representation of protein structures and a very common choice of cover image for a journal or textbook.

Current computer programs[edit]

PyMol ribbon of the structure of the tubby protein (PDB: 1C8Z​)

One popular program used for drawing ribbon diagrams is Molscript. Molscript utilizes Hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points (Cα atoms) guided by direction vectors. The program was built on the basis of traditional molecular graphics by Arthur M. Lesk, Karl Hardman, and John Priestle.[9] Jmol 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: urease) and MolMol (example: SH2 domain) also produce ribbon images. KiNG[10] is the Java-based successor to Mage (examples: α-hemolysin top view and side view).

UCSF Chimera is a powerful molecular modeling program that also includes visualizations such as ribbons, notable especially for the ability to combine them with contoured shapes from cryo-electron microscopy data.[11] PyMOL, by Warren DeLano,[12] is a very popular and flexible molecular graphics program (based on Python) that operates in interactive mode and also produces presentation-quality 2D images for ribbon diagrams and many other representations.

Features of ribbon diagrams[edit]

Spiral helix ribbons, beta-strand arrows, and smoothed loops, hand-drawn by Jane Richardson
Secondary Structure[4][5]
α-Helices Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides.
β-Strands Arrows with thickness, about one-quarter as thick as they are wide, shows direction and twist of the strand from amino to the carboxyl end. β-sheets are seen as unified, because neighboring strands twist in unison.
Loops and miscellaneous
Nonrepetitive loops Round ropes that are fatter in the foreground and thinner towards the back, following smoothed path of Cα trace.
Junctions between loops and helices Round rope that gradually flattens out into a thin helical ribbon.
Other features
Polypeptide direction,

NH2 and COOH termini

Small arrows on one or both of the termini or by 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.
Disulfide bonds Interlocked SS symbol or a zigzag, like a stylized lightning stroke.
Prosthetic groups or inhibitors Stick figures, or ball & stick.
Metals Spheres.
Shading and colour Shading or colour adds dimensionality to the diagram. Generally, the features at the front are the strongest, while becoming lower in contrast towards the back.

References[edit]

  1. ^ Smith, Thomas J. (October 27, 2005), Displaying and Analyzing Atomic Structures on the Macintosh 
  2. ^ Richardson, D. C.; Richardson, J. S. (2002), "Teaching Molecular 3-D Literacy", Biochemistry and Molecular Biology Education, 30: 21–26, doi:10.1002/bmb.2002.494030010005 .
  3. ^ a b Richardson, Jane S. (2000), "Early ribbon drawings of proteins", Nature Structural Biology, 7 (8): 624–625, PMID 10932243, doi:10.1038/77912 .
  4. ^ a b c Richardson, Jane S. (1985), "Schematic Drawings of Protein Structures", Methods in Enzymology, Methods in Enzymology, 115: 359–380, ISBN 978-0-12-182015-2, PMID 3853075, doi:10.1016/0076-6879(85)15026-3 .
  5. ^ a b Richardson, Jane S. (1981), "Anatomy and Taxonomy of Protein Structures", Advances in Protein Chemistry, Advances in Protein Chemistry, 34: 167–339, ISBN 978-0-12-034234-1, PMID 7020376, doi:10.1016/S0065-3233(08)60520-3 .
  6. ^ Lesk, Arthur M.; Hardman, Karl D. (1982), "Computer-Generated Schematic Diagrams of Protein Structures", Science, 216 (4545): 539–540, Bibcode:1982Sci...216..539L, PMID 7071602, doi:10.1126/science.7071602 .
  7. ^ 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 .
  8. ^ Richardson, D. C.; Richardson, J. S. (January 1992), "The kinemage: a tool for scientific communication", Protein Science, 1 (1): 3–9, PMC 2142077Freely accessible, PMID 1304880, doi:10.1002/pro.5560010102 
  9. ^ MolScript v2.1: About the program 
  10. ^ 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, PMC 2788294Freely accessible, PMID 19768809, doi:10.1002/pro.250 
  11. ^ 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, PMID 15766548, doi:10.1016/j.str.2005.01.006 .
  12. ^ Brunger, Axel T.; Wells, James A. (2009), "Warren L. DeLano, 21 June 1972-3 November 2009", Nature Structural & Molecular Biology, 16 (12): 1202–1203, PMID 19956203, doi:10.1038/nsmb1209-1202 .

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