a tool used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize 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.
