Modeling 3D Protein Structure using Chimera and Modeller
Homology or comparative protein structure modeling is a complex process, but with the help of tools like Modeller , it becomes more accessible and efficient. It's fascinating how the program can automatically calculate a model with all non-hydrogen atoms based on an alignment of a sequence to be modeled with known related structures. The input to Modeller are restraints on the spatial structure of the amino acid sequence(s) and ligands to be modeled, and the output is a 3D structure that satisfies these restraints as well as possible. It's amazing how the program can derive restraints from various sources such as related protein structures, NMR experiments, rules of secondary structure packing, cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, residue-residue and atom-atom potentials of mean force, and even intuition. The program can operate on various spatial features defined by atoms or pseudo at