Projects

Analysis of Intermediate Resolution Structures

The AIRS toolkit is developed within EMAN in order to analyze biological complexes at subnanometer resolutions. The AIRS package incorporates Helixhunter and Foldhunter for identification of helices and user specified folds, respectively. Additionally, new features such as sheet identification and image filtering have also been incorporated into the AIRS package. Like all other EMAN programs, the programs within AIRS are executable from the command line. Facilitating use, a graphical interface has been developed within UCSF's Visualization package, Chimera. In such, AIRS provides a relatively robust toolkit to interface and analyze subnanoemter resolution structures determined by electron cryomicroscopy.

contact: Matthew Baker, Ph.D.

Modeller

MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (2, 3), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is written in Fortran 90 and runs on the Pentium PC's (Linux and Win XP), Apple Macintosh (OS X) and workstations from Silicon Graphics (IRIX), Sun (Solaris), IBM (AIX), and DEC Alpha (OSF/1).

Volume Rover