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{{Jmol Applications Sections}}

This section is devoted to published articles and books that describe Jmol features or uses.

Please add additional literature (sorted on descending publication year):


=== 2017 ===
* Johannes Pernaa, Maija Aksela and Shenelle Pearl Ghulam: '''Introduction to Molecular Modeling in Chemistry Education'''. e-Oppi Ltd. & Edumendo Publishing, 2017; 120 pp. ISBN 978-952-6649-94-8 (ePub), ISBN 978-952-6649-93-1 (paperback). Details at: [http://publishing.edumendo.fi/post/introduction-to-molecular-modeling-in-chemistry-education bit.ly/immice]
: A small introductional book for molecular modeling in chemistry education, using JSmol. It includes theoretical background suitable for chemistry teachers, chemistry educational researchers and chemistry teachers students, and about 20 exercises that can be used in e.g. teacher training. It is being used as a part of a course material in an undergraduate molecular modeling and visualizaton course for chemistry teachers students. 
* Robert M. Hanson and Xiang-Jun Lu: '''DSSR-enhanced visualization of nucleic acid structures in Jmol'''. ''Nucleic Acids Research'' 2017, gkx365 (2017) doi:10.1093/nar/gkx365 Open access article.

=== 2016 ===
* Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, and Jason E. Bara: '''Programmatic conversion of crystal structures into 3D printable files using Jmol'''. ''Journal of Cheminformatics'' 8, 66 (2016) doi:10.1186/s13321-016-0181-z Open access article.
* Robert M. Hanson: '''Jmol SMILES and Jmol SMARTS: specifications and applications'''. ''Journal of Cheminformatics'' 8, 50 (2016) doi:10.1186/s13321-016-0160-4 Open access article.

=== 2013 ===
* Robert M. Hanson, Jaime Prilusky, Zhou Renjian, Takanori Nakane and Joel L. Sussman: '''JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia'''. ''Israel Journal of Chemistry'' 53, 207-216 (2013). doi:10.1002/ijch.201300024
*: [http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300024/abstract Abstract and article]
*: Also featured in the [http://onlinelibrary.wiley.com/doi/10.1002/ijch.201390002/abstract cover picture], ''Israel Journal of Chemistry'' 53 (3-4) 2013. doi:10.1002/ijch.201390002
* H. S. Rzepa, "Chemical datuments as scientific enablers", ''J. Chemoinformatics'', '''2013''', ''4'' 10.1186/1758-2946-5-6
* H. S. Rzepa, "Changing ways of sharing research in Chemistry", in "The future of scholarly communication: all change", M. Jubb and D. Shorley (Eds), 2013, ISBN 1-85604-817-0
* Shane P. Tully, Thomas M. Stitt, Robert D. Caldwell, Brian J. Hardock, Robert M. Hanson, and Przemyslaw Maslak: '''Interactive web-based pointillist visualization of hydrogenic orbitals using Jmol'''. ''Journal of Chemical Education'' 90, 129-131 (2013). doi:10.1021/ed300393s Article with complimentary full-text access.

=== 2011 ===
* Tim Wallace: '''Using Java applets to enhance online teaching and assessment in Blackboard'''. In ''Symposium on the Benefits of eLearning Technologies''. University of Manchester, 2011.
*: [http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf#page=12 Article]
* H. S. Rzepa, "The past, present and future of scientific discourse", ''J. Cheminformatics'', '''2011''', ''3'', 46. doi:10.1186/1758-2946-3-46

=== 2010 ===
* G. Rule, D. Bajzek & A. Kessler: '''Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform'''. In ''Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010'', pp. 304-309 (J. Sanchez & K. Zhang, eds.). Chesapeake, VA: AACE, 2010.
*: [http://telstar.ote.cmu.edu/biology/papers/ Abstract and article]
* Robert M. Hanson: '''''Jmol'' – a paradigm shift in crystallographic visualization'''. ''Journal of Applied Crystallography'', 43(5): 1250-1260 '''(2010)'''
*:doi:10.1107/S0021889810030256 - [http://dx.doi.org/10.1107/S0021889810030256 Abstract and article]
* J. H. Gutow, '''Easy Jmol Web Pages using the Jmol Export to Web Function.'''   ''Journal of Chemical Education WebWare''.  Publication Date (Web): April 8, 2010.
*: [http://pubs.acs.org/doi/abs/10.1021/ed100283v Link]
* O. Casher and H. S Rzepa, "Using Semantically-enabled Components for Social-Web based Scientific Collaborations", in "Enhancing Learning with Online Resources, Social Networking, and Digital Libraries", Editor(s): Robert E. Belford, John W. Moore, Harry E. Pence, 2010, DOI: 10.1021/bk-2010-1060.ch003.

=== 2009 ===
* Jeroen Logtenberg: '''Multi-user interaction with molecular visualizations on a multi-touch table.''' MSc Thesis, University of Twente, Enschede, The Netherlands '''(2009)'''. 
*: [http://purl.org/utwente/e59199 Full document]

=== 2008 ===
* Clifton Forlines, Ryan Lilien: '''Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment.''' In: ''Proceedings of the Working Conference on Advanced Visual Interfaces'', pp. 367-371 '''(2008)'''. 
*: doi:10.1145/1385569.1385635 - [http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf]
* Brian McMahon, Robert M. Hanson: '''A toolkit for publishing enhanced figures'''. ''Journal of Applied Crystallography'', 41(4): 811-814 '''(2008)'''
*:doi:10.1107/S0021889808015616 - [http://dx.doi.org/10.1107/S0021889808015616 Abstract and article]
* M. E. Cass and H. S. Rzepa, "Visualizing metal tris chelates - Visualizations to examine the structure and symmetry of metal tris chelates: Symmetry operations, chirality, and mechanisms (Bailar Twist and Ray-Dutt) that racemize the Δ and Λ isomers", J. Chem. Ed., 2008, 85, 750-751.

=== 2007 ===
* Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''. 
*: ''A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.'' - [http://biomodel.uah.es/Jmol-handbook.htm Info, preview and on-line shop] - ISBN 978-1-84799-259-8 <br />An update and an extra chapter: [http://www.lulu.com/product/15672160 Supplement 2011]

* Angel Herráez: '''Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''.
*: (In Spanish) - [http://biomodel.uah.es/Jmol-manual.htm Info, preview and on-line shop] - ISBN 978-1-84753-710-2

* Egon Willighagen, Miguel Howard: '''Fast and scriptable molecular graphics in web browsers without Java3D'''. ''Nature Precedings'' 14 June '''(2007)'''.
*: [http://dx.doi.org/10.1038/npre.2007.50.1 doi:10.1038/npre.2007.50.1]

* David A. Evans, Michael J. Bodkin, S. Richard Baker, Gary J. Sharman: '''Janocchio - a Java applet for viewing 3D structures and calculating NMR couplings and NOEs'''. ''Magnetic Resonance in Chemistry'' 45(7): 595-600 '''(2007)'''.
*: ''Janocchio is a Java applet based on Jmol; it calculates both H-H and H-C 3-bond coupling constants and NOEs from a three-dimensional structure.'' - [http://dx.doi.org/10.1002/mrc.2016 doi:10.1002/mrc.2016]
* H. S. Rzepa, "Achieving a Holistic Web in the chemistry curriculum", Ann. Rep. Comp. Chem., 2007, 3, 99-133.

=== 2006 ===
* Angel Herráez: '''Biomolecules in the computer:  Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(2006)'''.
*: ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://dx.doi.org/10.1002/bmb.2006.494034042644 doi:10.1002/bmb.2006.494034042644] - ''Now freely available in full-text.''

* '''Interview with Martin Walker'''. ''Reactive Reports'' 54 '''(2006)'''.
*: [http://www.reactivereports.com/54/54_0.html Article]

* Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend, Gilbert Vassart: '''GRIS: Glycoprotein-hormone Receptor Information System'''. ''Molecular Endocrinology'' 20(9): 2247-2255 '''(2006)'''.
*: doi:10.1210/me.2006-0020 - [http://mend.endojournals.org/cgi/content/abstract/me.2006-0020v1 Abstract and article]

=== 2005 ===
* Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. Williams: '''The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry'''. ''Journal of Chemical Education'' 82(11):1736-1740 '''(2005)'''.
*: [http://jchemed.chem.wisc.edu/Journal/Issues/2005/Nov/abs1736.html Abstract]

* Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny: '''CoC: a database of universally conserved residues in protein folds'''. ''Bioinformatics'' 21: 2539-2540 '''(2005)'''.
*: ''Describes the [http://kulibin.mit.edu/coc/ CoC database] which uses Jmol for visualisation.'' - doi:10.1093/bioinformatics/bti360 - [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/10/2539 Abstract]

* Egon Willighagen, Miguel Howard: '''Jmol as 3D Viewer for CDK'''. ''CDK News'' 2(1): 17-20 '''(2005)'''.
*: ''Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically.'' - [http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/ Article]

=== 2004 ===
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, Johann  Gasteiger: '''Enabling the exploration of biochemical pathways'''. ''Organic and Biomolecular Chemistry'' 2(2): 3226-3237 '''(2004)'''.
*: ''Introduces a [http://www2.chemie.uni-erlangen.de/services/biopath/ pathway] database that uses Jmol to visualize molecules.'' - doi:10.1039/B410949J - [http://www.rsc.org/Publishing/Journals/OB/article.asp?doi=B410949J Abstract and article]

* Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, Egon L. Willighagen: '''Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators'''. ''Journal of Chemical Information and Computer Sciences'' 44(2): 462-469 '''(2004)'''.
*: ''Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol.'' - doi:0.1021/ci034244p - [http://pubs.acs.org/cgi-bin/asap.cgi/jcisd8/asap/abs/ci034244p.html Abstract]

* Andreas Bohne-Lang, Elke Lang: '''3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets'''. ''BIOspektrum'' 2004(2): 167-169 '''(2004)'''.
*: ''Compares Jmol with other chemistry visualisation applets.'' - [http://www.elsevier.de/blatt/d_bs_download&_id=907283 Article]

=== 2003 ===
* Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen: '''The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics'''. ''Journal of Chemical Information and Computer Sciences'' 43(2): 493-500 '''(2003)'''.
*: ''Describes CDK, the library on which Jmol v6 to v9 is built.'' - doi:10.1021/ci025584y - [http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2003/43/i02/abs/ci025584y.html Abstract]

* Francis T. Marchese, Jude Mercado, Yi Pan: '''Adapting single-user visualization software for collaborative use.''' In: ''Proceedings of the Seventh International Conference on Information Visualization - An International Conference on Computer Visualization and Graphics Applications'', pp. 252-257 '''(2003)'''.
*: ISBN 0-7695-1988-1 - [http://csis.pace.edu/~marchese/Papers/IV03/marchese_iv03.pdf Article]

=== 2001 ===
* Egon L. Willighagen: '''Processing CML Conventions in Java'''. ''Internet Journal of Chemistry'' 4 '''(2001)'''.
*: ''Describes how Jmol upto and including v9 read CML.'' - [http://www.ijc.com/abstracts/abstract4n4.html Abstract]