RasMol & Educational Molecular Visualization Bibliography

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

Most recent first:

• J. Barrère, J-Y Dupont and N. Salamé : Structures et fonctions des molécules biologiques. Utilisations pédagogiques des visualisations tridimensionnelles avec Rasmol. INRP, 1997, 128 pages.

  1996

• 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

• 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.

• RasMol: Biomolecular graphics for all, by Roger A. Sayle and E. J. Milner-White, Trends in Biochemical Sciences 20(Sept):374-376, 1995.

• 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 63:1186-1209, 1992.

• The Kinemage: A tool for scientific communication, by David C. Richardson, and Jane S. Richardson, Protein Science 1:3-9, 1992.