Section 25.1.7.5.  MODELLER

MODELLER (Sali & Blundell, 1993) is most frequently used for homology or comparative modelling of protein three-dimensional structure. The user provides an alignment of a sequence to be modelled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints. In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modelling), NMR experiments (NMR refinement), rules of secondary-structure packing (combinatorial modelling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue–residue and atom–atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable-target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. MODELLER is also available as part of QUANTA (Section 25.1.7.8), Insight II (Section 25.1.7.3) and Weblab GeneExplorer.

Location: http://salilab.org/modeller/modeller.html . Operating system: UNIX. Type: source code and binary. Language: Fortran. Distribution: free academic.