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J Comput Chem. 2015 Feb 5;36(4):251-63. doi: 10.1002/jcc.23796. Epub 2014 Dec 2.

The Iterative Protein Redesign and Optimization (IPRO) suite of programs.

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Chemical Engineering Department, University of California, Santa Barbara, 3357 Engineering II, Santa Barbara, California, 93106.


Proteins are an important class of biomolecules with applications spanning across biotechnology and medicine. In many cases, native proteins must be redesigned to improve various performance metrics by changing their amino acid sequences. Algorithms can help sharpen protein library design by focusing the library on sequences that optimize computationally accessible proxies. The Iterative Protein Redesign and Optimization (IPRO) suite of programs offers an integrated environment for (1) altering protein binding affinity and specificity, (2) grafting a binding pocket into an existing protein scaffold, (3) predicting an antibody's tertiary structure based on its sequence, (4) enhancing enzymatic activity, and (5) assessing the structure and binding energetics for a specific mutant. This manuscript provides an overview of the methods involved in IPRO, input language terminology, algorithmic details, software implementation specifics and application highlights. IPRO can be downloaded at


IPRO; antibodies; computational design; enzymes; proteins

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