RasMol & Educational Molecular Visualization Bibliography

Historic references will be found under the History of Molecular Visualization.

Most recent first:

1997

• 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.

  1996

• Surprising similarities in structure comparison. Jean-François Gilbrat, Thomas Madej, and Stephen H. Bryant. Current Opinion 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 Information.

• 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, 1996. 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.

  1995

• 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. Illustrated.

• 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. Extensively illustrated.

• Kinemages: make your own molecules for teaching, by Charles W. Sokolik, Trends in Biochemical Sciences 20(March):122-4, 1995.

  1994

• 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.

  1992

• 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.