Software Tools For Molecular Microscopy
There are a large number of software tools or software applications that have been specifically developed for the field sometimes referred to as molecular microscopy or cryo-electron microscopy or cryoEM. Several special issues of the Journal of Structural Biology (see references below) have been specifically devoted to descriptions of these applications and several web sites provide partial lists of the software packages and where to obtain them. This article attempts to provide a complete list and up-to-date distribution information of all of the software of interest to the cryoEM community. Everyone in the community is encouraged to add content, correct errors, and make any other contributions that might be useful.
The software tools described here have been loosely and somewhat arbitrarily organized into several categories as follows:
- General packages: Packages that offer a comprehensive set of tools to permit the analysis of data in several classes of structural problems.
- Specific packages: Packages that offer a comprehensive set of tools to permit the analysis of data in a single class of structural problem. For example packages specifically focused on objects with helical, icosahedral, crystalline symmetry, etc.
- Application tools: Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc.
- Visualization and docking/modeling tools: Packages that facilitate the interpretation, analysis or presentation of the results.
- Utilities: General utilities like file format conversion, difference mapping, etc.
- Carragher B, Smith PR (1996). "Advances in computational image processing for microscopy". J. Struct. Biol. 116 (1): 2–8. doi:10.1006/jsbi.1996.0002. PMID 8742716.
- Smith R, Carragher B (September 2008). "Software tools for molecular microscopy". J. Struct. Biol. 163 (3): 224–8. doi:10.1016/j.jsb.2008.03.002. PMID 18406627.
- Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF (March 2005). "Electron cryomicroscopy of biological machines at subnanometer resolution". Structure 13 (3): 363–72. doi:10.1016/j.str.2004.12.016. PMID 15766537.
- Frank, Joachim (2006). Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state (2 ed.). Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-518218-9.
- A special issue of The Journal of Structural Biology that focuses specifically on Software Tools for Macromolecular Microscopy
- 3DEM mailing listThe 3DEM list is a primary communication source among experts in the field of molecular and cellular electron microscopy.
- EM for Dummies. Basics of electron microscopy in single particle reconstruction, and its applications to biology.
- EM Data Bank (EMDB) Archive of experimentally determined 3D maps and associated data.
- VIPERdb EM Database. Archive of icosahedral virus maps at the Virus Particle Explorer web site.
- 3DEM Conventions Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology.
- Journal of Structural Biology main page
- Voss et al. (2010) Software tools for molecular microscopy: an open-text Wikibook. Methods Enzymol 482, 381-392.