MODELLER

MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints. More generally, the input to the program are restraints on the spatial structure of the amino acid sequence(s) and ligands to be modeled. The output is a 3-D structure that satisfies these restraints as well as possible. Restraints can in principle be derived from a number of different sources, including related protein structures (comparative modeling). MODELLER can also perform multiple comparison of protein sequences and/or structures, clustering of proteins, and searching of sequence databases. The 3-D model is obtained by optimization of a molecular probability density function (pdf). The molecular pdf for comparative modeling is optimized with the variable target function procedure in Cartesian space that employs methods of conjugate gradients and molecular dynamics with simulated annealing. The program is used with a scripting language and does not include any graphics. open in new windowMODELLER web site.