kinemage
{{Short description|Interactive graphic scientific illustration}}
File:RibonucleaseA ribbon 7rsa.jpg ribbons, from a kinemage displayed in Mage: β-strands are green, helices gold, and active-site His sidechains blue.]]
A kinemage (short for kinetic image) is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can also represent other types of 3-dimensional data (such as geometric figures, social networks,{{cite journal
| first = L. C.
| last = Freeman
|author2=hierarchy
| year = 1998
| title = Exploring social structure using dynamic three-dimensional color images
| journal = Social Networks
| volume = 20
| pages = 109–118
| doi =10.1016/S0378-8733(97)00016-6
| issue = 2
|display-authors=etal| url = http://moreno.ss.uci.edu/77.pdf
}} or tetrahedra of [http://www.santafe.edu/~pth/simplex.html/ RNA base composition]). The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the file extension '.kin'.
Early history
Kinemages were first developed by David Richardson at Duke University School of Medicine, for the Protein Society's journal Protein Science that premiered in January 1992.{{cite journal
| first = D. C.
| last = Richardson
| authorlink = Jane S. Richardson
|author2=J.S. Richardson
|date=January 1992
| title = The kinemage: a tool for scientific communication
| journal = Protein Science
| volume = 1
| issue = 1
| pages = 3–9
| doi =10.1002/pro.5560010102
| pmid = 1304880
| pmc = 2142077
}} For its first 5 years (1992–1996), each issue of Protein Science included a supplement on floppy disk of interactive, kinemage 3D computer graphics to illustrate many of the articles, plus the Mage software (cross-platform, free, open-source) to display them;{{cite journal
| first = H.
| last = Neurath
| authorlink = Hans Neurath
| year = 1992
| title = Editorial. The Kinemage: A Tool for Scientific Illustration
| journal = Protein Science
| volume = 5
| issue = 11
| pages = 2147
| doi =10.1002/pro.5560051101
| pmc = 2143300
}} kinemage supplementary material is still available on the journal web site. Mage and RasMol{{cite book
| first = R.
| last = Sayle
| year = 1992
| title = Proceedings of the 10th Eurographics UK 1992 Conference
| publisher = Abingdon Press, York
| doi =
}} were the first widely used macromolecular graphics programs to support interactive display on personal computers. Kinemages are used for teaching,{{cite journal
| first = D. C.
| last = Richardson
|author2=J.S. Richardson
| year = 1994
| title = Kinemages - Simple Macromolecular Graphics for Interactive Teaching and Publication
| journal = Trends in Biochemical Sciences
| volume = 19
| pages = 135–138
| doi =10.1016/0968-0004(94)90207-0| pmid = 8203021
| issue = 3
| first = D. C.
| last = Richardson
|author2=J.S. Richardson
| year = 2002
| title = Teaching Molecular 3-D Literacy
| journal = Biochemistry and Molecular Biology Education
| volume = 30
| pages = 21–26
| doi =10.1002/bmb.2002.494030010005
| doi-access = free
}} and for textbook supplements,{{cite book
| first = D.
| last = Voet
|author2=J. G. Voet |author3=C. W. Pratt
| year = 1999
| title = Fundamentals of Biochemistry
| url = https://archive.org/details/fundamentalsofbi00voet
| url-access = registration
| publisher = John Wiley & Sons, New York
| doi =
| first = C.-I.
| last = Branden
|author2=J. Tooze
| year = 1999
| title = Introduction to Protein Structure
| edition = 2
| publisher = Garland Publishing, Inc., New York
| doi =
}} individual exploration, and analysis of macromolecular structures.
File:RibonucleaseA Uvan inhibitor contacts 1ruv.jpg and the Uridine Vanadate transition-state-mimic inhibitor (PDB file 1RUV), with hydrogen bonds as pillows of pale green dots and favorable van der Waals contacts in blue and green.]]
Research uses
More recently, with the availability of a much wider variety of other molecular graphics tools, presentation use of kinemages has been overtaken by a wide variety of research uses, concomitant with new display features and with the development of software that produces kinemage-format output from other types of molecular calculations. All-atom contact analysis{{cite journal
| first = J. M.
| last = Word
| year = 1999
| title = Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms
| journal = Journal of Molecular Biology
| volume = 285
| pages = 1711–1733
| doi = 10.1006/jmbi.1998.2400
| pmid = 9917407
| issue = 4
|display-authors=etal| citeseerx = 10.1.1.119.6173
}} adds and optimizes explicit hydrogen atoms,{{cite journal
| first = J. M.
| last = Word
| year = 1999
| title = Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation
| journal = Journal of Molecular Biology
| volume = 285
| pages = 1735–1747
| doi = 10.1006/jmbi.1998.2401
| pmid = 9917408
| issue = 4
|display-authors=etal| citeseerx = 10.1.1.323.6971
}} and then uses patches of dot surface to display the hydrogen bond, van der Waals, and steric clash interactions between atoms. The results can be used visually (in kinemages) and quantitatively to analyze the detailed interactions between molecular surfaces,{{cite journal
| first = J. M.
| last = Word
| year = 2000
| title = Exploring steric constraints on protein mutations using MAGE/PROBE
| journal = Protein Science
| volume = 9
| pages = 2251–2259
| doi =10.1110/ps.9.11.2251
| pmid = 11152136
| issue = 11
| pmc = 2144501
|display-authors=etal}}{{cite journal
| first = J. S.
| last = Richardson
| authorlink = Jane S. Richardson
|author2=Richardson, D.C.
| year = 2002
| title = Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
| journal = Proc. Natl. Acad. Sci. USA
| volume = 99
| pages = 2754–2759
| doi = 10.1073/pnas.052706099
| pmid = 11880627
| issue = 5
| pmc = 122420
| bibcode = 2002PNAS...99.2754R
| doi-access = free
}} most extensively for the purpose of validating and improving the molecular models from experimental x-ray crystallography data.{{cite journal
| first = D. C.
| last = Richardson
|author2=Richardson, J. S.
| year = 2001
| title = MAGE, PROBE, and Kinemages
| journal = International Tables for Crystallography
| volume = F, chapter 25.2.8
| pages = 727–730
| doi =
| first1 = Jane S.
| last1 = Richardson
| display-authors=1
| last2=Arendall III
| first2 =W. Bryan
| year = 2003
| volume = 374
| pages = 385–412
| doi =10.1016/S0076-6879(03)74018-X
| pmid = 14696383
| series = Methods in Enzymology
| isbn = 978-0-12-182777-9
| last3 = Richardson
| first3 = David C.
| title = Macromolecular Crystallography, Part D
| chapter = New Tools and Data for Improving Structures, Using All-Atom Contacts
| first = V.A..
| last = Higman
| year = 2004
| title = Asparagine and glutamine side-chain conformations in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings
| journal = Journal of Biomolecular NMR
| volume = 30
| pages = 327–346
| doi =10.1007/s10858-004-3218-y
| pmid = 15754058
| issue = 3
| s2cid = 26047711
|display-authors=etal}}{{cite journal
| first = W. B.
| last = Arendall III
| year = 2005
| title = A test of enhancing model accuracy in high-throughput crystallography
| journal = Journal of Structural and Functional Genomics
| volume = 6
| issue = 1
| pages = 1–11
| doi = 10.1007/s10969-005-3138-4
| pmid = 15965733
| s2cid = 2790812
|display-authors=etal}} Both Mage and KiNG (see below) have been enhanced for kinemage display of data in higher than 3 dimensions (moving between views in various 3-D projections, coloring and selecting candidate clusters of datapoints, and switching to a parallel coordinates representation), used for instance for defining clusters of favorable RNA backbone conformations in the 7-dimensional space of backbone dihedral angles between one ribose and the next.{{cite journal
| first = J. S.
| last = Richardson
| year = 2008
| title = RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
| journal = RNA
| volume = 14
| pages = 465–481
| doi = 10.1261/rna.657708
| pmid = 18192612
| issue = 3
| pmc = 2248255
|display-authors=etal}}
Online web use
KiNG is an open-source kinemage viewer, written in the programming language Java by Ian Davis and Vincent Chen,{{cite journal|year=2009|title= KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program |journal=Protein Science|volume=18|pages=2403–2409|doi= 10.1002/pro.250|pmid=19768809|issue=11|pmc=2788294|author=Chen, V.B.|display-authors=etal}} that can work interactively either standalone on a user machine with no network connection, or as a web service in a web page. The interactive nature of kinemages is their primary purpose and attribute. To appreciate their nature, the demonstration KiNG in browser has two examples that can be moved around in 3D, plus instructions for how to embed a kinemage on a web page.[http://kinemage.biochem.duke.edu/software/kingInBrowser/KiNGinBrowser_object.html KiNG in browser] The figure below shows KiNG being used to remodel a lysine sidechain in a high-resolution crystal structure. KiNG is one of the viewers provided on each structure page at the Protein Data Bank site,{{Cite web |url=http://www.rcsb.org/pdb/ |title=Protein Data Bank |access-date=2016-12-07 |archive-url=https://web.archive.org/web/20080828002005/http://www.rcsb.org/pdb/ |archive-date=2008-08-28 |url-status=dead }} and displays validation results in 3D on the MolProbity site.[http://molprobity.biochem.duke.edu/ MolProbity]{{cite journal
| first = I. W.
| last = Davis
| authorlink =
| year = 2007
| title = MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
| journal = Nucleic Acids Research
| volume = 35
| issue = Web server issue
| pages = W375–W383
| doi = 10.1093/nar/gkm216
| id =
| url =
| format =
| accessdate =
| quote =
| pmid = 17452350
| pmc = 1933162
|display-authors=etal}}{{cite journal
| first = V. B.
| last = Chen
| authorlink =
| year = 2010
| title = MolProbity: all-atom structure validation for macromolecular crystallography
| journal = Acta Crystallographica
| volume = D 66
| pages = 12–21
| doi = 10.1107/S0907444909042073
| pmid = 20057044
| issue = Pt 1
| pmc = 2803126|display-authors=etal}} Kinemages can also be shown in immersive virtual reality systems, with the open-source KinImmerse software.{{cite journal
| first1 = J. N.
| last1 = Block
| display-authors=1
| last2=Zielinski
| first2=D. J.
| year = 2009
| title = KinImmerse: Macromolecular VR for NMR ensembles
| journal = Source Code for Biology and Medicine
| volume = 4
| doi = 10.1186/1751-0473-4-3
| pmid = 19222844
| pages = 3
| pmc = 2650690| last3 = Chen
| first3 = V. B.
| last4 = Davis
| first4 = I. W.
| last5 = Vinson
| first5 = E. C.
| last6 = Brady
| first6 = R.
| last7 = Richardson
| first7 = J. S.
| last8 = Richardson
| first8 = D. C.
| doi-access = free
}} All of the kinemage display and all-atom contact software is available free and open-source on the [http://kinemage.biochem.duke.edu kinemage web site].
See also
References
{{Reflist}}
External links
- {{Official website|kinemage.biochem.duke.edu}}, Duke University original, with examples and software
- [http://kinemage.biochem.duke.edu/gallery/ kinemage example in a browser]
- [https://web.archive.org/web/20080828002005/http://www.rcsb.org./pdb RCSB Protein Data Bank]
- [http://molprobity.biochem.duke.edu MolProbity: structure validation, with KiNG on-line kinemages]