RasMol & Educational Molecular Visualization Bibliography
A list of publications (on paper!) concerning RasMol and other free
molecular visualization software.
For the primary reference for RasMol, see
Please send comments or additions to firstname.lastname@example.org).
Historic references will be found under the
History of Molecular Visualization.
Most recent first:
Structures et fonctions des
molécules biologiques. Utilisations pédagogiques des visualisations
tridimensionnelles avec Rasmol.
J. Barrère, J-Y Dupont and N. Salamé.
INRP, 1997, 128 pages.
Surprising similarities in structure comparison.
Jean-François Gilbrat, Thomas Madej, and Stephen H. Bryant.
in Structural Biology 6:377-385, 1996.
A review of early results of searcing for similarities in structure,
regardless of sequence similarities. Describes the Vector Alignment
Search Tool (VAST) provided by the US National Center for Biotechnology
- GlaxoWellcome and MDL become entangled in the Web, by John
Hodgson, Nature Biotechnology 14:690, June 1996.
This article concerning RasMol and Chime is full of errors. See the editorial comment.
A Dynamic Look at Structures: WWW-Entrez and the Molecular Modeling
Database, by Christopher W. V. Hogue, Hitomi Ohkawa and Stephen
H. Bryant. Trends in Biochemical Sciences, 21:226-9,
All PDB files have been converted to the WWW-Entrez format ASN.1. This
format can handle a broader range of 3D structural information, including for
example models from electron microscopy. WWW-Entrez links 3D structural
information with GenBank sequences and MEDLINE abstracts. Related structures
can be identified. Kinemage animations are generated automatically to
reveal information buried in PDB files, such as thermal factors, disordered
zones, and multiple NMR models.
- RasMol: Biomolecular graphics for all, by Roger A. Sayle and
E. James Milner-White, Trends in Biochemical Sciences
20(Sept):374-376, 1995. RasMol was first widely
distributed via the Internet in June, 1993, but this is the original
paper publication describing RasMol.
Hyperactive Molecules and the World-Wide-Web Information
System, by Omer Casher, Gudge K. Chandramohan, Martin J.
Hargreaves, Christopher Leach, Peter Murray-Rust, Henry S. Rzepa,
Roger A. Sayle and Benjamin J. Whitaker. J. Chem. Soc., Perkin Trans.
2, 1995, 7.
This paper proposes sharing chemical data too bulky for journal
publication via World Wide Web. To accomplish this, it introduces
various new chemical MIME (Multipurpose Internet Mail Extension) types,
including chemical/x-csml for the Chemical Structure Markup
Language which can be understood by RasMol.
- Software for viewing biomolecules in three dimensions on the
Internet, by Alvaro Sanchez-Ferrer, Estrella Nunez-Delicado, and Roque
Bru, Trends in Biochemical Sciences 20(July):286-288,
1995. Compares RasMol 2.5, pdVwin, Pkin_2_4/Mage_2_4, Hyperchem 3.0.
- Utilisations pédagogiques des visualisations
tridimensionelles de molécules en biologie, by J.
Barrère, J.-Y. Dupont, and N. Salamé, in Images
numériques dan l'enseignement des sciences, Journées
d'études CNAM, June 1995, J. C. Le Touzé and N.
Salamé, eds., Institut Nationale de Recherche
Pédagogique, pp. 87-93. A brief introduction to the use of
RasMol for educational molecular visualization of DNA and proteins,
touching on hemoglobin and the active site of carboxypeptidase.
- Logiciels de visualisation tridimensionnelle de
molécules, by J. Barrère, J.-Y. Dupont, and N.
Salamé, Activités Pratiques Biologie Géologie
Bull. 4:725-753, 1995. Introduces RasMol and MAGE.
Proposes detailed tutorials on DNA, hemoglobin with the sickle mutation
and hemoglobin evolution, antibody structure, and lysozyme evolution.
- Kinemages: make your own molecules for teaching, by Charles W.
Sokolik, Trends in Biochemical Sciences 20(March):122-4,
- Kinemages -- simple macromolecular graphics for interactive teaching
and publication, by David C. Richardson and Jane S. Richardson,
Trends in Biochemical Sciences 19(March):135-8, 1994.
- Looking at proteins: representations, folding, packing, and design.
Biophysical Society National Lecture. Richardson, J. S., Richardson, D. C.,
Tweedy, N. B., Gernert, K. M., Quinn, T. P., Hect, M. H., Erickson, B. W., Yan,
Y., McClain, R. D., Donlan, M. E., and Surles, M. C. Biophysical
Journal 63(November):1186-1209, 1992.
This is the paper which begins famously "Protein crystallography is
rather like a dog chasing cars." A fascinating and entertaining
tour of protein structure, making comparisons to origami, an Italian castle,
and a Greek vase. Another incisive quote:
CPK models are very informative during the process of putting them
together, but the completed models all look alike. Computer
versions of CPK models have successfully imitated their appearance
and most of their disadvantages (the fact that the inside is
completely hidden, and the difficulty of identifying an atom or
group), without, so far, imitating the real virtue of CPK's, which
is the physical "feel" for the bumps, constraints, and degrees of
freedom one obtains by manipulating them.
- The Kinemage: A tool for scientific communication, by David C. Richardson,
and Jane S. Richardson, Protein Science 1:3-9, 1992.
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