Difference between revisions of "Literature"

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=== 2008 ===
 
=== 2008 ===
  
* C. Forlines, R. 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'', 2008, pp. 367-371. doi:10.1145/1385569.1385635 [http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf Article]
+
* C. Forlines, R. 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'', 2008, pp. 367-371.  
 +
*: doi:10.1145/1385569.1385635 - [http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf Article]
  
 
* B. McMahon and Robert M. Hanson: '''A toolkit for publishing enhanced figures'''. ''Journal of Applied Crystallography'', 41(4): 811-814 '''(2008)'''
 
* B. McMahon and 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]
+
*:doi:10.1107/S0021889808015616 - [http://dx.doi.org/10.1107/S0021889808015616 Abstract and article]
  
 
=== 2007 ===
 
=== 2007 ===
  
* Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. <nowiki>ISBN 978-1-84799-259-8</nowiki>. Published by Lulu.com '''(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]
+
*: ''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
  
* Angel Herráez: '''Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1'''. <nowiki>ISBN 978-1-84753-710-2</nowiki>. Published by Lulu.com '''(2007)'''.
+
* 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]
+
*: (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]
+
* 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]
  
 
* D.A. Evans, M.J. Bodkin, S.R. Baker & G.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)'''.
 
* D.A. Evans, M.J. Bodkin, S.R. Baker & G.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]
+
*: ''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]
  
 
=== 2006 ===
 
=== 2006 ===
  
 
* Angel Herráez: '''Biomolecules in the computer:  Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(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.''
+
*: ''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)'''.
 
* '''Interview with Martin Walker'''. ''Reactive Reports'' 54 '''(2006)'''.
Line 34: Line 36:
  
 
* Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart: '''GRIS: Glycoprotein-hormone Receptor Information System'''. ''Molecular Endocrinology'' 20(9): 2247-2255 '''(2006)'''.
 
* Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and 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]
+
*: doi:10.1210/me.2006-0020 - [http://mend.endojournals.org/cgi/content/abstract/me.2006-0020v1 Abstract and article]
  
 
=== 2005 ===
 
=== 2005 ===
Line 42: Line 44:
  
 
* Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich and Leonid A. Mirny: '''CoC: a database of universally conserved residues in protein folds'''. ''Bioinformatics'' 21: 2539-2540 '''(2005)'''.
 
* Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich and Leonid A. Mirny: '''CoC: a database of universally conserved residues in protein folds'''. ''Bioinformatics'' 21: 2539-2540 '''(2005)'''.
*: ''Described 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]
+
*: ''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 and Miguel Howard: '''Jmol as 3D Viewer for CDK'''. ''CDK News'' 2(1): 17-20 '''(2005)'''.
 
* Egon Willighagen and 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]
+
*: ''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 ===
 
=== 2004 ===
  
 
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger: '''Enabling the exploration of biochemical pathways'''. ''Organic and Biomolecular Chemistry'' 2(2): 3226-3237 '''(2004)'''.
 
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. 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]
+
*: ''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, and 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)'''.
 
* Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, and 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]
+
*: ''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, and Elke Lang: '''3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets'''. ''BIOspektrum'' 2004(2): 167-169 '''(2004)'''.
 
* Andreas Bohne-Lang, and 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]
+
*: ''Compares Jmol with other chemistry visualisation applets.'' - [http://www.elsevier.de/blatt/d_bs_download&_id=907283 Article]
  
 
=== 2003 ===
 
=== 2003 ===
  
 
* Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, and 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)'''.
 
* Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, and 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]
+
*: ''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]
  
* F.T. Marchese, J. Mercado, Y. 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'', 2003, pp. 252-257. ISBN 0-7695-1988-1. [http://csis.pace.edu/~marchese/Papers/IV03/marchese_iv03.pdf Article]
+
* F.T. Marchese, J. Mercado, Y. 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'', 2003, pp. 252-257.
 +
*: ISBN 0-7695-1988-1 - [http://csis.pace.edu/~marchese/Papers/IV03/marchese_iv03.pdf Article]
  
 
=== 2001 ===
 
=== 2001 ===
  
 
* E.L. Willighagen: '''Processing CML Conventions in Java'''. ''Internet Journal of Chemistry'' 4 '''(2001)'''.
 
* E.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]
+
*: ''Describes how Jmol upto and including v9 read CML.'' - [http://www.ijc.com/abstracts/abstract4n4.html Abstract]

Revision as of 15:34, 12 January 2009

Jmol / JSmol Applications

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

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

2008

  • C. Forlines, R. 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, 2008, pp. 367-371.
    doi:10.1145/1385569.1385635 - Article
  • B. McMahon and Robert M. Hanson: A toolkit for publishing enhanced figures. Journal of Applied Crystallography, 41(4): 811-814 (2008)
    doi:10.1107/S0021889808015616 - Abstract and article

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. - Info, preview and on-line shop - ISBN 978-1-84799-259-8
  • Angel Herráez: Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1. Lulu Enterprises: Morrisville, NC, USA (2007).
    (In Spanish) - 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).
    doi:10.1038/npre.2007.50.1
  • D.A. Evans, M.J. Bodkin, S.R. Baker & G.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. - doi:10.1002/mrc.2016

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. doi:10.1002/bmb.2006.494034042644 - Now freely available in full-text.
  • Interview with Martin Walker. Reactive Reports 54 (2006).
    Article
  • Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart: GRIS: Glycoprotein-hormone Receptor Information System. Molecular Endocrinology 20(9): 2247-2255 (2006).
    doi:10.1210/me.2006-0020 - Abstract and article

2005

  • M.E. Cass, H.S. Rzepa, D.R. Rzepa, and C.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).
    Abstract
  • Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich and Leonid A. Mirny: CoC: a database of universally conserved residues in protein folds. Bioinformatics 21: 2539-2540 (2005).
    Describes the CoC database which uses Jmol for visualisation. - doi:10.1093/bioinformatics/bti360 - Abstract
  • Egon Willighagen and 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. - Article

2004

  • Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger: Enabling the exploration of biochemical pathways. Organic and Biomolecular Chemistry 2(2): 3226-3237 (2004).
    Introduces a pathway database that uses Jmol to visualize molecules. - doi:10.1039/B410949J - Abstract and article
  • Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, and 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 - Abstract
  • Andreas Bohne-Lang, and Elke Lang: 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets. BIOspektrum 2004(2): 167-169 (2004).
    Compares Jmol with other chemistry visualisation applets. - Article

2003

  • Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, and 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 - Abstract
  • F.T. Marchese, J. Mercado, Y. 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, 2003, pp. 252-257.
    ISBN 0-7695-1988-1 - Article

2001

  • E.L. Willighagen: Processing CML Conventions in Java. Internet Journal of Chemistry 4 (2001).
    Describes how Jmol upto and including v9 read CML. - Abstract