Department of Biology, Johns Hopkins University, 1969
Eric Martz, Ph.D.
Department of Microbiology
203 Morrill Science Center IVN
University of Massachusetts
639 North Pleasant Street
Amherst, MA 01003-9298
Our work provides innovative, widely-used, award-winning tools for visualization of macromolecular structures in education, research, and structural bioinformatics. These are all free and open source, and include:
- FirstGlance in Jmol (firstglance.jmol.org): A simple 3D visualization tool for web browsers, designed for journals that publish new protein structures. Requires no installation. Adopted by Nature among others. Free and open-source, first offered in 2005.
- Proteopedia.Org is a wiki (a user-annotated website) that connects interactive 3D molecular structure views to explanatory text. It was created in 2007 by Joel Sussman, Eran Hodis, and Jaime Prilusky at the Weizmann Institute of Science, Rehovot, Israel. Martz joined their team in 2008, and has contributed many articles. [Hodis et al., 2008.]
- The ConSurf Server (consurf.tau.ac.il) automatically identifies evolutionarily conserved surface patches on proteins. Developed by Nir Ben-Tal, Fabian Glaser, Tal Pupko, Elana Erez et al. at Tel-Aviv University, Israel. Martz integrated 3D visualization, initially with Protein Explorer, and later with FirstGlance in Jmol. First available Fall 2002. [Landau et al., 2005; Glaser et al., 2003.]
MolviZ.org: Educational Macromolecular Visualization Tutorials & Resources including structures of DNA, hemoglobin, antibody, MHC, lipid bilayers and channels, water, and more. Portions first offered in 1996. MolviZ.org domain name starting fall 2004. Includes:
- Top Five Molecular Visualization Resources for the Rest Of Us (top5.molviz.org): Tutorials, Exploration Tools, & Communication Tools that work on Windows and Mac OS X without installing anything (except java), and will remain available for years to come. (None of these resources uses MDL Chime.)
- High School Teachers' Molecular Visualization Resources (highschool.molviz.org): Designed for high school teachers, working on Windows and Mac OS X, nothing to install.
- Our illustrated Atlas of Macromolecules (atlas.molviz.org) provides a handy source of examples to educators and students. First available in 2002.
- Short Courses in Practical Macromolecular Visualization and Structural Bioinformatics (workshops.molviz.org) can be arranged.
- The World Index of Molecular Visualization Resources (molvisindex.org): a visitor-maintained database, first offered in 2000.
- Protein Explorer (proteinexplorer.org): Popular 1998-2006 for exploring, understanding, and qualitative analysis of structures of proteins and protein-ligand or protein-drug interactions. MERLOT Classic Award for Biology in 2003: "has revolutionized the teaching of biology at a molecular level". Adopted as a visualization option by several bioinformatics resources. First offered in 1998; developed until 2007, when the MDL Chime plugin upon which it depends became increasingly problematic. [Martz, 2002.]
- PDB Lite (pdblite.org), mirrored worldwide, helps beginners find published protein structures. First available 1998.
- The Molecular Visualization Freeware EMail Discussion provides an international forum for educators and developers. Founded 1995.
- RasMol Classic Site provides the most complete documentation available for RasMol 2.6, a popular macromolecular visualization tool by Roger A. Sayle. Website developed 1995-2000. Subsequent RasMol development: rasmol.org.