The September 2012 special issue of Biopolymers "2010 Cryo-EM Modeling Challenge" is now online. The issue contents include an editorial and eight articles describing results from the 2010 cryo-EM modeling challenge. The publications describe current major approaches to interpretation of cryo-EM reconstructions, including segmentation, secondary structure detection, rigid-body docking, flexible fitting, ab initio protein modeling, and refinement. The collection serves to establish capabilities of current modeling methods and to provide guidance on how to proceed with map interpretation at various resolution ranges.