Difference between revisions of "Literature"

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Please add additional literature (sorted on descending publication year):
 
Please add additional literature (sorted on descending publication year):
  
 +
* Angel Herráez, Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1, '''2007''', <nowiki>ISBN 978-1-84753-710-2</nowiki>. Published by Lulu.com
 +
** (In Spanish; English translation in preparation) ''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://stores.lulu.com/angel_herraez info, preview and on-line shop]
 
* Angel Herráez, Biomolecules in the computer:  Jmol to the rescue, ''Biochemistry and Molecular Biology Education'', '''2006''', 34(4): 255-261.
 
* Angel Herráez, Biomolecules in the computer:  Jmol to the rescue, ''Biochemistry and Molecular Biology Education'', '''2006''', 34(4): 255-261.
*: ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://www.bambed.org/cgi/content/abstract/34/4/255 abstract]
+
** ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://www.bambed.org/cgi/content/abstract/34/4/255 abstract]
 
* [http://www.reactivereports.com/54/54_0.html Interview with Martin Walker], ''Reactive Reports'', '''2006'''.
 
* [http://www.reactivereports.com/54/54_0.html Interview with Martin Walker], ''Reactive Reports'', '''2006'''.
 
* Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart, GRIS: Glycoprotein-hormone Receptor Information System., ''Molecular Endocrinology'', '''2006''', doi:10.1210/me.2006-0020 (Rapid Electronic Publication). The article can be downloaded [http://mend.endojournals.org/cgi/content/abstract/me.2006-0020v1 here].
 
* Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart, GRIS: Glycoprotein-hormone Receptor Information System., ''Molecular Endocrinology'', '''2006''', doi:10.1210/me.2006-0020 (Rapid Electronic Publication). The article can be downloaded [http://mend.endojournals.org/cgi/content/abstract/me.2006-0020v1 here].
 
* M.E. Cass, H.S. Rzepa, D.R. Rzepa, '''et al.''', The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry, ''Journal of Chemical Education'', '''2005''', 82(11):1736-1740
 
* M.E. Cass, H.S. Rzepa, D.R. Rzepa, '''et al.''', The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry, ''Journal of Chemical Education'', '''2005''', 82(11):1736-1740
 
* 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'', '''2005''', vol 21, 2539-2540
 
* 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'', '''2005''', vol 21, 2539-2540
*: ''Described the [http://kulibin.mit.edu/coc/ CoC database] which uses Jmol for visualisation. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/10/2539 abstract]''
+
** ''Described the [http://kulibin.mit.edu/coc/ CoC database] which uses Jmol for visualisation. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/10/2539 abstract]''
 
* Egon Willighagen and Miguel Howard, Jmol as 3D Viewer for CDK, ''CDK News'', '''2005''', vol 2, issue 1, 17-20
 
* Egon Willighagen and Miguel Howard, Jmol as 3D Viewer for CDK, ''CDK News'', '''2005''', vol 2, issue 1, 17-20
*: ''Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. The article can be downloaded [http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/ here].''
+
** ''Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. The article can be downloaded [http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/ here].''
 
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger, Enabling the exploration of biochemical pathways, ''Org.Biomol.Chem.'', '''2004''', 3226-3237
 
* Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger, Enabling the exploration of biochemical pathways, ''Org.Biomol.Chem.'', '''2004''', 3226-3237
*: ''Introduces a [http://www2.chemie.uni-erlangen.de/services/biopath/ pathway] database that uses Jmol to visualize molecules.''
+
** ''Introduces a [http://www2.chemie.uni-erlangen.de/services/biopath/ pathway] database that uses Jmol to visualize molecules.''
 
* 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, ''J.Chem.Inf.Comp.Sci.'', '''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, ''J.Chem.Inf.Comp.Sci.'', '''2004'''
*: ''Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol [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 [http://pubs.acs.org/cgi-bin/asap.cgi/jcisd8/asap/abs/ci034244p.html abstract].''
 
* Anreas Bohne-Lang, and Elke Lang, 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets, ''BIOspektrum'', '''2004'''
 
* Anreas Bohne-Lang, and Elke Lang, 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets, ''BIOspektrum'', '''2004'''
*: ''Compares Jmol with other chemistry visualisation applets.''
+
** ''Compares Jmol with other chemistry visualisation applets.''
 
* 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, ''J.Chem.Inf.Comp.Sci.'', '''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, ''J.Chem.Inf.Comp.Sci.'', '''2003'''
*: ''Describes CDK the library on which Jmol v6 to v9 is build [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 build [http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2003/43/i02/abs/ci025584y.html abstract].''
 
* 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 19:15, 22 September 2007

Jmol / JSmol Applications

Jmol Literature

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

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

  • Angel Herráez, Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1, 2007, ISBN 978-1-84753-710-2. Published by Lulu.com
    • (In Spanish; English translation in preparation) 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
  • Angel Herráez, Biomolecules in the computer: Jmol to the rescue, Biochemistry and Molecular Biology Education, 2006, 34(4): 255-261.
    • A review of Jmol project and features, in comparison to Rasmol and Chime. abstract
  • Interview with Martin Walker, Reactive Reports, 2006.
  • Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart, GRIS: Glycoprotein-hormone Receptor Information System., Molecular Endocrinology, 2006, doi:10.1210/me.2006-0020 (Rapid Electronic Publication). The article can be downloaded here.
  • M.E. Cass, H.S. Rzepa, D.R. Rzepa, et al., The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry, Journal of Chemical Education, 2005, 82(11):1736-1740
  • 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, 2005, vol 21, 2539-2540
  • Egon Willighagen and Miguel Howard, Jmol as 3D Viewer for CDK, CDK News, 2005, vol 2, issue 1, 17-20
    • Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. The article can be downloaded here.
  • Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger, Enabling the exploration of biochemical pathways, Org.Biomol.Chem., 2004, 3226-3237
    • Introduces a pathway database that uses Jmol to visualize molecules.
  • 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, J.Chem.Inf.Comp.Sci., 2004
    • Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol abstract.
  • Anreas Bohne-Lang, and Elke Lang, 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets, BIOspektrum, 2004
    • Compares Jmol with other chemistry visualisation applets.
  • 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, J.Chem.Inf.Comp.Sci., 2003
    • Describes CDK the library on which Jmol v6 to v9 is build abstract.
  • E.L. Willighagen, Processing CML Conventions in Java, Internet Journal of Chemistry, 4, 2001
    • Describes how Jmol upto and including v9 read CML abstract.