The preceding discussion implicitly assumed that the rotamers are all different orientations of the same amino acid side chain. That is, the sequence of the protein was assumed to be fixed. It is also possible to allow multiple side chains to "compete" over a position by including both types of side chains in the set of rotamers for that position. This allows a novel sequence to be designed onto a given protein backbone. A short zinc finger protein fold has been redesigned this way. However, this greatly increases the number of rotamers per position and still requires a fixed protein length.
Read more about this topic: Dead-end Elimination
Other articles related to "protein design, protein, proteins, design":
... Iterative Protein Redesign and Optimization ... IPRO redesigns proteins to increase or give specificity to native or novel substrates and cofactors ... repeatedly randomly perturbing the backbones of the proteins around specified design positions, identifying the lowest energy combination of rotamers, and ...
... Further information Protein structure prediction, Protein docking, Protein design With the proliferation of genome sequencing projects, scientists can infer the amino acid sequence, or primary ... To better understand a protein's function and aid in rational drug design, scientists need to know the protein's three-dimensional tertiary structure ... Protein 3D structures are currently determined experimentally through X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy ...
... In rational protein design, the scientist uses detailed knowledge of the structure and function of the protein to make desired changes ... However, its major drawback is that detailed structural knowledge of a protein is often unavailable, and even when it is available, it can be extremely difficult to predict the ... Computational protein design algorithms seek to identify novel amino acid sequences that are low in energy when folded to the pre-specified target structure ...
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