MODELLER is used for homology or comparative modeling of protein
three-dimensional structures. 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, 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.